# Copyright 2022 by Michiel de Hoon.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Align.sam module."""
import unittest
from io import StringIO

from Bio import Align
from Bio import SeqIO
from Bio.Align import Alignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

try:
    import numpy as np
except ImportError:
    from Bio import MissingPythonDependencyError

    raise MissingPythonDependencyError(
        "Install numpy if you want to use Bio.Align.sam."
    ) from None


class TestAlign_dna_rna(unittest.TestCase):
    # The SAM file dna_rna.sam was generated using these commands:
    # twoBitToFa hg38.2bit stdout | samtools dict -a hg38 -s "Homo sapiens" | grep -v chrUn | grep -v alt | grep -v random > dna_rna.sam
    # psl2sam.pl dna_rna.psl >> dna_rna.sam
    # The CIGAR string was then edited to replace D by N for introns and H by S
    # where appropriate.
    # The alignment scores (AS tag) were copied from the BED file dna_rna.bed.

    def setUp(self):
        data = {}
        records = SeqIO.parse("Blat/dna.fa", "fasta")
        for record in records:
            name, start_end = record.id.split(":")
            assert name == "chr3"
            start, end = start_end.split("-")
            start = int(start)
            end = int(end)
            sequence = str(record.seq).upper()
            assert len(sequence) == end - start
            data[start] = sequence
        self.dna = Seq(data, length=198295559)
        records = SeqIO.parse("Blat/rna.fa", "fasta")
        self.rna = {record.id: record.seq for record in records}
        self.rna["NR_111921.1"] = self.rna["NR_111921.1"][:-12]
        self.rna["NR_111921.1_modified"] = self.rna["NR_111921.1_modified"][:-12]
        # Last 12 nucleotides were clipped by Blat as the poly(A) tail

    def check_alignments(self, alignments):
        """Check the alignments."""
        self.assertEqual(list(alignments.metadata), ["HD"])
        self.assertEqual(alignments.metadata["HD"], {"VN": "1.0", "SO": "unsorted"})
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 248956422)
        self.assertEqual(
            alignments.targets[0].annotations,
            {
                "MD5": "2648ae1bacce4ec4b6cf337dcae37816",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[1].id, "chr10")
        self.assertEqual(len(alignments.targets[1]), 133797422)
        self.assertEqual(
            alignments.targets[1].annotations,
            {
                "MD5": "907112d17fcb73bcab1ed1c72b97ce68",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[2].id, "chr11")
        self.assertEqual(len(alignments.targets[2]), 135086622)
        self.assertEqual(
            alignments.targets[2].annotations,
            {
                "MD5": "1511375dc2dd1b633af8cf439ae90cec",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[3].id, "chr12")
        self.assertEqual(len(alignments.targets[3]), 133275309)
        self.assertEqual(
            alignments.targets[3].annotations,
            {
                "MD5": "e81e16d3f44337034695a29b97708fce",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[4].id, "chr13")
        self.assertEqual(len(alignments.targets[4]), 114364328)
        self.assertEqual(
            alignments.targets[4].annotations,
            {
                "MD5": "17dab79b963ccd8e7377cef59a54fe1c",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[5].id, "chr14")
        self.assertEqual(len(alignments.targets[5]), 107043718)
        self.assertEqual(
            alignments.targets[5].annotations,
            {
                "MD5": "acbd9552c059d9b403e75ed26c1ce5bc",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[6].id, "chr15")
        self.assertEqual(len(alignments.targets[6]), 101991189)
        self.assertEqual(
            alignments.targets[6].annotations,
            {
                "MD5": "f036bd11158407596ca6bf3581454706",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[7].id, "chr16")
        self.assertEqual(len(alignments.targets[7]), 90338345)
        self.assertEqual(
            alignments.targets[7].annotations,
            {
                "MD5": "24e7cabfba3548a2bb4dff582b9ee870",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[8].id, "chr17")
        self.assertEqual(len(alignments.targets[8]), 83257441)
        self.assertEqual(
            alignments.targets[8].annotations,
            {
                "MD5": "a8499ca51d6fb77332c2d242923994eb",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[9].id, "chr18")
        self.assertEqual(len(alignments.targets[9]), 80373285)
        self.assertEqual(
            alignments.targets[9].annotations,
            {
                "MD5": "11eeaa801f6b0e2e36a1138616b8ee9a",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[10].id, "chr19")
        self.assertEqual(len(alignments.targets[10]), 58617616)
        self.assertEqual(
            alignments.targets[10].annotations,
            {
                "MD5": "b0eba2c7bb5c953d1e06a508b5e487de",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[11].id, "chr2")
        self.assertEqual(len(alignments.targets[11]), 242193529)
        self.assertEqual(
            alignments.targets[11].annotations,
            {
                "MD5": "4bb4f82880a14111eb7327169ffb729b",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[12].id, "chr20")
        self.assertEqual(len(alignments.targets[12]), 64444167)
        self.assertEqual(
            alignments.targets[12].annotations,
            {
                "MD5": "b18e6c531b0bd70e949a7fc20859cb01",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[13].id, "chr21")
        self.assertEqual(len(alignments.targets[13]), 46709983)
        self.assertEqual(
            alignments.targets[13].annotations,
            {
                "MD5": "2f45a3455007b7e271509161e52954a9",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[14].id, "chr22")
        self.assertEqual(len(alignments.targets[14]), 50818468)
        self.assertEqual(
            alignments.targets[14].annotations,
            {
                "MD5": "221733a2a15e2de66d33e73d126c5109",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[15].id, "chr3")
        self.assertEqual(len(alignments.targets[15]), 198295559)
        self.assertEqual(
            alignments.targets[15].annotations,
            {
                "MD5": "a48af509898d3736ba95dc0912c0b461",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[16].id, "chr4")
        self.assertEqual(len(alignments.targets[16]), 190214555)
        self.assertEqual(
            alignments.targets[16].annotations,
            {
                "MD5": "3210fecf1eb92d5489da4346b3fddc6e",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[17].id, "chr5")
        self.assertEqual(len(alignments.targets[17]), 181538259)
        self.assertEqual(
            alignments.targets[17].annotations,
            {
                "MD5": "f7f05fb7ceea78cbc32ce652c540ff2d",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[18].id, "chr6")
        self.assertEqual(len(alignments.targets[18]), 170805979)
        self.assertEqual(
            alignments.targets[18].annotations,
            {
                "MD5": "6a48dfa97e854e3c6f186c8ff973f7dd",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[19].id, "chr7")
        self.assertEqual(len(alignments.targets[19]), 159345973)
        self.assertEqual(
            alignments.targets[19].annotations,
            {
                "MD5": "94eef2b96fd5a7c8db162c8c74378039",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[20].id, "chr8")
        self.assertEqual(len(alignments.targets[20]), 145138636)
        self.assertEqual(
            alignments.targets[20].annotations,
            {
                "MD5": "c67955b5f7815a9a1edfaa15893d3616",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[21].id, "chr9")
        self.assertEqual(len(alignments.targets[21]), 138394717)
        self.assertEqual(
            alignments.targets[21].annotations,
            {
                "MD5": "addd2795560986b7491c40b1faa3978a",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[22].id, "chrM")
        self.assertEqual(len(alignments.targets[22]), 16569)
        self.assertEqual(
            alignments.targets[22].annotations,
            {
                "MD5": "c68f52674c9fb33aef52dcf399755519",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[23].id, "chrX")
        self.assertEqual(len(alignments.targets[23]), 156040895)
        self.assertEqual(
            alignments.targets[23].annotations,
            {
                "MD5": "49527016a48497d9d1cbd8e4a9049bd3",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        self.assertEqual(alignments.targets[24].id, "chrY")
        self.assertEqual(len(alignments.targets[24]), 57227415)
        self.assertEqual(
            alignments.targets[24].annotations,
            {
                "MD5": "b2b7e6369564d89059e763cd6e736837",
                "assembly": "hg38",
                "species": "Homo sapiens",
            },
        )
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 1711))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr3")
        self.assertEqual(alignment.query.id, "NR_046654.1")
        self.assertEqual(len(alignment.target.seq), len(self.dna))
        self.assertEqual(
            alignment.target.seq.defined_ranges,
            ((42530895, 42530958), (42532020, 42532095), (42532563, 42532606)),
        )
        for start, end in alignment.target.seq.defined_ranges:
            self.assertEqual(alignment.target.seq[start:end], self.dna[start:end])
        self.assertEqual(alignment.query.seq, self.rna[alignment.query.id])
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606],
                          [     181,      118,      118,       43,       43,        0]])
                # fmt: on
            )
        )
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
                np.array([[38.,  0.,  0.,  0.],
                          [ 0., 41.,  0.,  0.],
                          [ 0.,  0., 60.,  0.],
                          [ 0.,  0.,  0., 42.],
                         ])
                # fmt: on
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGT")
        self.assertEqual(alignment.mapq, 0)
        matches = sum(
            alignment.substitutions[c, c] for c in alignment.substitutions.alphabet
        )
        self.assertEqual(alignment.score, 1000)
        self.assertEqual(alignment.annotations["NM"], 0)
        self.assertNotIn("hard_clip_left", alignment.query.annotations)
        self.assertNotIn("hard_clip_right", alignment.query.annotations)
        self.assertEqual(alignment.operations, bytearray(b"MNMNM"))
        self.assertEqual(
            str(alignment),
            """\
chr3       42530895 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC
                  0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NR_046654       181 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC

chr3       42530955 AGG?????????????????????????????????????????????????????????
                 60 |||---------------------------------------------------------
NR_046654       121 AGG---------------------------------------------------------

chr3       42531015 ????????????????????????????????????????????????????????????
                120 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531075 ????????????????????????????????????????????????????????????
                180 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531135 ????????????????????????????????????????????????????????????
                240 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531195 ????????????????????????????????????????????????????????????
                300 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531255 ????????????????????????????????????????????????????????????
                360 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531315 ????????????????????????????????????????????????????????????
                420 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531375 ????????????????????????????????????????????????????????????
                480 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531435 ????????????????????????????????????????????????????????????
                540 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531495 ????????????????????????????????????????????????????????????
                600 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531555 ????????????????????????????????????????????????????????????
                660 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531615 ????????????????????????????????????????????????????????????
                720 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531675 ????????????????????????????????????????????????????????????
                780 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531735 ????????????????????????????????????????????????????????????
                840 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531795 ????????????????????????????????????????????????????????????
                900 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531855 ????????????????????????????????????????????????????????????
                960 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531915 ????????????????????????????????????????????????????????????
               1020 ------------------------------------------------------------
NR_046654       118 ------------------------------------------------------------

chr3       42531975 ?????????????????????????????????????????????CAGTTCTTCCTTGAG
               1080 ---------------------------------------------|||||||||||||||
NR_046654       118 ---------------------------------------------CAGTTCTTCCTTGAG

chr3       42532035 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC
               1140 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NR_046654       103 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC

chr3       42532095 ????????????????????????????????????????????????????????????
               1200 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532155 ????????????????????????????????????????????????????????????
               1260 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532215 ????????????????????????????????????????????????????????????
               1320 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532275 ????????????????????????????????????????????????????????????
               1380 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532335 ????????????????????????????????????????????????????????????
               1440 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532395 ????????????????????????????????????????????????????????????
               1500 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532455 ????????????????????????????????????????????????????????????
               1560 ------------------------------------------------------------
NR_046654        43 ------------------------------------------------------------

chr3       42532515 ????????????????????????????????????????????????CTAGCATCCTTC
               1620 ------------------------------------------------||||||||||||
NR_046654        43 ------------------------------------------------CTAGCATCCTTC

chr3       42532575 CCAGGTATGCATCTGCTGCCAAGCCAGGGAG 42532606
               1680 |||||||||||||||||||||||||||||||     1711
NR_046654        31 CCAGGTATGCATCTGCTGCCAAGCCAGGGAG        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
NR_046654.1	16	chr3	42530896	0	63M1062N75M468N43M	*	0	0	CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCCAGGCAGTTCTTCCTTGAGCGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGACCTAGCATCCTTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG	*	AS:i:1000	NM:i:0
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (181 aligned letters; 181 identities; 0 mismatches; 1530 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 181:
        identities = 181,
        mismatches = 0.
    gaps = 1530:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 1530:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 1530:
                open_internal_deletions = 2,
                extend_internal_deletions = 1528;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 1530)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 1530)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 1530)
        self.assertEqual(counts.gaps, 1530)
        self.assertEqual(counts.aligned, 181)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 1714))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr3")
        self.assertEqual(alignment.query.id, "NR_046654.1_modified")
        self.assertEqual(len(alignment.target.seq), len(self.dna))
        self.assertEqual(
            alignment.target.seq.defined_ranges,
            ((42530895, 42530958), (42532020, 42532095), (42532563, 42532606)),
        )
        for start, end in alignment.target.seq.defined_ranges:
            self.assertEqual(alignment.target.seq[start:end], self.dna[start:end])
        self.assertEqual(alignment.query.seq, self.rna[alignment.query.id])
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42530895, 42530922, 42530922, 42530958, 42532020,
                           42532037, 42532039, 42532095, 42532563, 42532606],
                          [     185,      158,      155,      119,      119,
                                102,      102,       46,       46,        3],
                         ])
                # fmt: on
            )
        )
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
                np.array([[36.,  0.,  0.,  1.],
                          [ 0., 41.,  0.,  0.],
                          [ 0.,  0., 60.,  0.],
                          [ 0.,  0.,  0., 41.],
                         ]),
                # fmt: on
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGT")
        self.assertEqual(alignment.mapq, 0)
        self.assertEqual(alignment.score, 978)
        self.assertEqual(alignment.annotations["NM"], 6)
        self.assertNotIn("hard_clip_left", alignment.query.annotations)
        self.assertNotIn("hard_clip_right", alignment.query.annotations)
        self.assertEqual(alignment.operations, bytearray(b"MIMNMDMNM"))
        self.assertEqual(
            str(alignment),
            """\
chr3       42530895 CGGAAGTACTTCTGGGGGTACATACTC---ATCGGCTGGGGTATGGTACCAGGGAGGGCT
                  0 |||||||||||||||||||||||||||---||||||||||||||||||||||||||||||
NR_046654       185 CGGAAGTACTTCTGGGGGTACATACTCCCCATCGGCTGGGGTATGGTACCAGGGAGGGCT

chr3       42530952 TCCAGG??????????????????????????????????????????????????????
                 60 ||||||------------------------------------------------------
NR_046654       125 TCCAGG------------------------------------------------------

chr3       42531012 ????????????????????????????????????????????????????????????
                120 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531072 ????????????????????????????????????????????????????????????
                180 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531132 ????????????????????????????????????????????????????????????
                240 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531192 ????????????????????????????????????????????????????????????
                300 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531252 ????????????????????????????????????????????????????????????
                360 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531312 ????????????????????????????????????????????????????????????
                420 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531372 ????????????????????????????????????????????????????????????
                480 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531432 ????????????????????????????????????????????????????????????
                540 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531492 ????????????????????????????????????????????????????????????
                600 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531552 ????????????????????????????????????????????????????????????
                660 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531612 ????????????????????????????????????????????????????????????
                720 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531672 ????????????????????????????????????????????????????????????
                780 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531732 ????????????????????????????????????????????????????????????
                840 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531792 ????????????????????????????????????????????????????????????
                900 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531852 ????????????????????????????????????????????????????????????
                960 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531912 ????????????????????????????????????????????????????????????
               1020 ------------------------------------------------------------
NR_046654       119 ------------------------------------------------------------

chr3       42531972 ????????????????????????????????????????????????CAGTTCTTCCTT
               1080 ------------------------------------------------||||||||||||
NR_046654       119 ------------------------------------------------CAGTTCTTCCTT

chr3       42532032 GAGCGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT
               1140 |||||--|||||||||||.|||||||||||||||||||||||||||||||||||||||||
NR_046654       107 GAGCG--AGCGGATTGGGTGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT

chr3       42532092 GAC?????????????????????????????????????????????????????????
               1200 |||---------------------------------------------------------
NR_046654        49 GAC---------------------------------------------------------

chr3       42532152 ????????????????????????????????????????????????????????????
               1260 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532212 ????????????????????????????????????????????????????????????
               1320 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532272 ????????????????????????????????????????????????????????????
               1380 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532332 ????????????????????????????????????????????????????????????
               1440 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532392 ????????????????????????????????????????????????????????????
               1500 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532452 ????????????????????????????????????????????????????????????
               1560 ------------------------------------------------------------
NR_046654        46 ------------------------------------------------------------

chr3       42532512 ???????????????????????????????????????????????????CTAGCATCC
               1620 ---------------------------------------------------|||||||||
NR_046654        46 ---------------------------------------------------CTAGCATCC

chr3       42532572 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG 42532606
               1680 ||||||||||||||||||||||||||||||||||     1714
NR_046654        37 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG        3
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
NR_046654.1_modified	16	chr3	42530896	0	5S27M3I36M1062N17M2D56M468N43M3S	*	0	0	AAAAACGGAAGTACTTCTGGGGGTACATACTCCCCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCCAGGCAGTTCTTCCTTGAGCGAGCGGATTGGGTGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGACCTAGCATCCTTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAGAAA	*	AS:i:978	NM:i:6
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (179 aligned letters; 178 identities; 1 mismatches; 1535 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 179:
        identities = 178,
        mismatches = 1.
    gaps = 1535:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 1535:
            internal_insertions = 3:
                open_internal_insertions = 1,
                extend_internal_insertions = 2;
            internal_deletions = 1532:
                open_internal_deletions = 3,
                extend_internal_deletions = 1529;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 3)
        self.assertEqual(counts.internal_deletions, 1532)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 1535)
        self.assertEqual(counts.insertions, 3)
        self.assertEqual(counts.deletions, 1532)
        self.assertEqual(counts.gaps, 1535)
        self.assertEqual(counts.aligned, 179)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 5407))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr3")
        self.assertEqual(alignment.query.id, "NR_111921.1")
        self.assertEqual(len(alignment.target.seq), len(self.dna))
        self.assertEqual(
            alignment.target.seq.defined_ranges,
            ((48663767, 48663813), (48665640, 48665722), (48669098, 48669174)),
        )
        for start, end in alignment.target.seq.defined_ranges:
            self.assertEqual(alignment.target.seq[start:end], self.dna[start:end])
        self.assertEqual(alignment.query.seq, self.rna[alignment.query.id])
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array( [[48663767, 48663813, 48665640, 48665722, 48669098, 48669174],
                              [       0,        46,      46,      128,      128,      204]]),
                # fmt: on
            )
        )
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
                np.array([[62.,  0.,  0.,  0.],
                          [ 0., 42.,  0.,  0.],
                          [ 0.,  0., 66.,  0.],
                          [ 0.,  0.,  0., 34.],
                         ])
                # fmt: on
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGT")
        self.assertEqual(alignment.mapq, 0)
        self.assertEqual(alignment.score, 1000)
        self.assertEqual(alignment.annotations["NM"], 0)
        self.assertNotIn("hard_clip_left", alignment.query.annotations)
        self.assertEqual(alignment.query.annotations["hard_clip_right"], 12)
        self.assertEqual(alignment.operations, bytearray(b"MNMNM"))
        self.assertEqual(
            str(alignment),
            """\
chr3       48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG??????????????
                  0 ||||||||||||||||||||||||||||||||||||||||||||||--------------
NR_111921         0 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG--------------

chr3       48663827 ????????????????????????????????????????????????????????????
                 60 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48663887 ????????????????????????????????????????????????????????????
                120 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48663947 ????????????????????????????????????????????????????????????
                180 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664007 ????????????????????????????????????????????????????????????
                240 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664067 ????????????????????????????????????????????????????????????
                300 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664127 ????????????????????????????????????????????????????????????
                360 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664187 ????????????????????????????????????????????????????????????
                420 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664247 ????????????????????????????????????????????????????????????
                480 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664307 ????????????????????????????????????????????????????????????
                540 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664367 ????????????????????????????????????????????????????????????
                600 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664427 ????????????????????????????????????????????????????????????
                660 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664487 ????????????????????????????????????????????????????????????
                720 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664547 ????????????????????????????????????????????????????????????
                780 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664607 ????????????????????????????????????????????????????????????
                840 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664667 ????????????????????????????????????????????????????????????
                900 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664727 ????????????????????????????????????????????????????????????
                960 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664787 ????????????????????????????????????????????????????????????
               1020 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664847 ????????????????????????????????????????????????????????????
               1080 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664907 ????????????????????????????????????????????????????????????
               1140 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48664967 ????????????????????????????????????????????????????????????
               1200 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665027 ????????????????????????????????????????????????????????????
               1260 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665087 ????????????????????????????????????????????????????????????
               1320 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665147 ????????????????????????????????????????????????????????????
               1380 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665207 ????????????????????????????????????????????????????????????
               1440 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665267 ????????????????????????????????????????????????????????????
               1500 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665327 ????????????????????????????????????????????????????????????
               1560 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665387 ????????????????????????????????????????????????????????????
               1620 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665447 ????????????????????????????????????????????????????????????
               1680 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665507 ????????????????????????????????????????????????????????????
               1740 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665567 ????????????????????????????????????????????????????????????
               1800 ------------------------------------------------------------
NR_111921        46 ------------------------------------------------------------

chr3       48665627 ?????????????CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
               1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
NR_111921        46 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC

chr3       48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGG?????????????????????????
               1920 |||||||||||||||||||||||||||||||||||-------------------------
NR_111921        93 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGG-------------------------

chr3       48665747 ????????????????????????????????????????????????????????????
               1980 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48665807 ????????????????????????????????????????????????????????????
               2040 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48665867 ????????????????????????????????????????????????????????????
               2100 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48665927 ????????????????????????????????????????????????????????????
               2160 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48665987 ????????????????????????????????????????????????????????????
               2220 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666047 ????????????????????????????????????????????????????????????
               2280 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666107 ????????????????????????????????????????????????????????????
               2340 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666167 ????????????????????????????????????????????????????????????
               2400 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666227 ????????????????????????????????????????????????????????????
               2460 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666287 ????????????????????????????????????????????????????????????
               2520 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666347 ????????????????????????????????????????????????????????????
               2580 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666407 ????????????????????????????????????????????????????????????
               2640 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666467 ????????????????????????????????????????????????????????????
               2700 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666527 ????????????????????????????????????????????????????????????
               2760 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666587 ????????????????????????????????????????????????????????????
               2820 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666647 ????????????????????????????????????????????????????????????
               2880 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666707 ????????????????????????????????????????????????????????????
               2940 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666767 ????????????????????????????????????????????????????????????
               3000 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666827 ????????????????????????????????????????????????????????????
               3060 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666887 ????????????????????????????????????????????????????????????
               3120 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48666947 ????????????????????????????????????????????????????????????
               3180 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667007 ????????????????????????????????????????????????????????????
               3240 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667067 ????????????????????????????????????????????????????????????
               3300 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667127 ????????????????????????????????????????????????????????????
               3360 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667187 ????????????????????????????????????????????????????????????
               3420 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667247 ????????????????????????????????????????????????????????????
               3480 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667307 ????????????????????????????????????????????????????????????
               3540 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667367 ????????????????????????????????????????????????????????????
               3600 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667427 ????????????????????????????????????????????????????????????
               3660 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667487 ????????????????????????????????????????????????????????????
               3720 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667547 ????????????????????????????????????????????????????????????
               3780 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667607 ????????????????????????????????????????????????????????????
               3840 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667667 ????????????????????????????????????????????????????????????
               3900 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667727 ????????????????????????????????????????????????????????????
               3960 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667787 ????????????????????????????????????????????????????????????
               4020 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667847 ????????????????????????????????????????????????????????????
               4080 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667907 ????????????????????????????????????????????????????????????
               4140 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48667967 ????????????????????????????????????????????????????????????
               4200 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668027 ????????????????????????????????????????????????????????????
               4260 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668087 ????????????????????????????????????????????????????????????
               4320 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668147 ????????????????????????????????????????????????????????????
               4380 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668207 ????????????????????????????????????????????????????????????
               4440 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668267 ????????????????????????????????????????????????????????????
               4500 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668327 ????????????????????????????????????????????????????????????
               4560 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668387 ????????????????????????????????????????????????????????????
               4620 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668447 ????????????????????????????????????????????????????????????
               4680 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668507 ????????????????????????????????????????????????????????????
               4740 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668567 ????????????????????????????????????????????????????????????
               4800 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668627 ????????????????????????????????????????????????????????????
               4860 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668687 ????????????????????????????????????????????????????????????
               4920 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668747 ????????????????????????????????????????????????????????????
               4980 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668807 ????????????????????????????????????????????????????????????
               5040 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668867 ????????????????????????????????????????????????????????????
               5100 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668927 ????????????????????????????????????????????????????????????
               5160 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48668987 ????????????????????????????????????????????????????????????
               5220 ------------------------------------------------------------
NR_111921       128 ------------------------------------------------------------

chr3       48669047 ???????????????????????????????????????????????????AGACGGGAG
               5280 ---------------------------------------------------|||||||||
NR_111921       128 ---------------------------------------------------AGACGGGAG

chr3       48669107 CTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATAT
               5340 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NR_111921       137 CTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATAT

chr3       48669167 TAAAAAA 48669174
               5400 |||||||     5407
NR_111921       197 TAAAAAA      204
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
NR_111921.1	0	chr3	48663768	0	46M1827N82M3376N76M12H	*	0	0	CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGCTGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGGAGACGGGAGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATATTAAAAAA	*	AS:i:1000	NM:i:0
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (204 aligned letters; 204 identities; 0 mismatches; 5203 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 204:
        identities = 204,
        mismatches = 0.
    gaps = 5203:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 5203:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 5203:
                open_internal_deletions = 2,
                extend_internal_deletions = 5201;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 5203)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 5203)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 5203)
        self.assertEqual(counts.gaps, 5203)
        self.assertEqual(counts.aligned, 204)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 5409))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr3")
        self.assertEqual(alignment.query.id, "NR_111921.1_modified")
        self.assertEqual(len(alignment.target.seq), len(self.dna))
        self.assertEqual(
            alignment.target.seq.defined_ranges,
            ((48663767, 48663813), (48665640, 48665722), (48669098, 48669174)),
        )
        for start, end in alignment.target.seq.defined_ranges:
            self.assertEqual(alignment.target.seq[start:end], self.dna[start:end])
        self.assertEqual(alignment.query.seq, self.rna[alignment.query.id])
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48663767, 48663795, 48663796, 48663813, 48665640,
                           48665716, 48665716, 48665722, 48669098, 48669174],
                          [       3,       31,       31,       48,       48,
                                124,      126,      132,      132,      208],
                         ])
                # fmt: on
            )
        )
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
                np.array([[62.,  0.,  0.,  0.],
                          [ 0., 41.,  0.,  0.],
                          [ 0.,  2., 64.,  0.],
                          [ 0.,  0.,  0., 34.],
                         ]),
                # fmt: on
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGT")
        self.assertEqual(alignment.mapq, 0)
        self.assertEqual(alignment.score, 972)
        self.assertEqual(alignment.annotations["NM"], 5)
        self.assertNotIn("hard_clip_left", alignment.query.annotations)
        self.assertEqual(alignment.query.annotations["hard_clip_right"], 12)
        self.assertEqual(alignment.operations, bytearray(b"MDMNMIMNM"))
        self.assertEqual(
            str(alignment),
            """\
chr3       48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG??????????????
                  0 ||||||||||||||||||||||||||||-|||||||||||||||||--------------
NR_111921         3 CACGAGAGGAGCGGAGGCGAGGGGTGAA-GCGGAGCACTCCAATCG--------------

chr3       48663827 ????????????????????????????????????????????????????????????
                 60 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48663887 ????????????????????????????????????????????????????????????
                120 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48663947 ????????????????????????????????????????????????????????????
                180 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664007 ????????????????????????????????????????????????????????????
                240 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664067 ????????????????????????????????????????????????????????????
                300 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664127 ????????????????????????????????????????????????????????????
                360 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664187 ????????????????????????????????????????????????????????????
                420 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664247 ????????????????????????????????????????????????????????????
                480 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664307 ????????????????????????????????????????????????????????????
                540 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664367 ????????????????????????????????????????????????????????????
                600 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664427 ????????????????????????????????????????????????????????????
                660 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664487 ????????????????????????????????????????????????????????????
                720 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664547 ????????????????????????????????????????????????????????????
                780 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664607 ????????????????????????????????????????????????????????????
                840 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664667 ????????????????????????????????????????????????????????????
                900 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664727 ????????????????????????????????????????????????????????????
                960 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664787 ????????????????????????????????????????????????????????????
               1020 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664847 ????????????????????????????????????????????????????????????
               1080 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664907 ????????????????????????????????????????????????????????????
               1140 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48664967 ????????????????????????????????????????????????????????????
               1200 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665027 ????????????????????????????????????????????????????????????
               1260 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665087 ????????????????????????????????????????????????????????????
               1320 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665147 ????????????????????????????????????????????????????????????
               1380 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665207 ????????????????????????????????????????????????????????????
               1440 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665267 ????????????????????????????????????????????????????????????
               1500 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665327 ????????????????????????????????????????????????????????????
               1560 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665387 ????????????????????????????????????????????????????????????
               1620 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665447 ????????????????????????????????????????????????????????????
               1680 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665507 ????????????????????????????????????????????????????????????
               1740 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665567 ????????????????????????????????????????????????????????????
               1800 ------------------------------------------------------------
NR_111921        48 ------------------------------------------------------------

chr3       48665627 ?????????????CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
               1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
NR_111921        48 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC

chr3       48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAG--ACCAGG???????????????????????
               1920 |||||..||||||||||||||||||||||--||||||-----------------------
NR_111921        95 TGCTGCCCGGCAGATGGAGCGATCAGAAGCCACCAGG-----------------------

chr3       48665745 ????????????????????????????????????????????????????????????
               1980 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48665805 ????????????????????????????????????????????????????????????
               2040 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48665865 ????????????????????????????????????????????????????????????
               2100 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48665925 ????????????????????????????????????????????????????????????
               2160 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48665985 ????????????????????????????????????????????????????????????
               2220 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666045 ????????????????????????????????????????????????????????????
               2280 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666105 ????????????????????????????????????????????????????????????
               2340 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666165 ????????????????????????????????????????????????????????????
               2400 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666225 ????????????????????????????????????????????????????????????
               2460 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666285 ????????????????????????????????????????????????????????????
               2520 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666345 ????????????????????????????????????????????????????????????
               2580 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666405 ????????????????????????????????????????????????????????????
               2640 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666465 ????????????????????????????????????????????????????????????
               2700 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666525 ????????????????????????????????????????????????????????????
               2760 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666585 ????????????????????????????????????????????????????????????
               2820 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666645 ????????????????????????????????????????????????????????????
               2880 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666705 ????????????????????????????????????????????????????????????
               2940 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666765 ????????????????????????????????????????????????????????????
               3000 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666825 ????????????????????????????????????????????????????????????
               3060 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666885 ????????????????????????????????????????????????????????????
               3120 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48666945 ????????????????????????????????????????????????????????????
               3180 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667005 ????????????????????????????????????????????????????????????
               3240 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667065 ????????????????????????????????????????????????????????????
               3300 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667125 ????????????????????????????????????????????????????????????
               3360 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667185 ????????????????????????????????????????????????????????????
               3420 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667245 ????????????????????????????????????????????????????????????
               3480 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667305 ????????????????????????????????????????????????????????????
               3540 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667365 ????????????????????????????????????????????????????????????
               3600 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667425 ????????????????????????????????????????????????????????????
               3660 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667485 ????????????????????????????????????????????????????????????
               3720 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667545 ????????????????????????????????????????????????????????????
               3780 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667605 ????????????????????????????????????????????????????????????
               3840 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667665 ????????????????????????????????????????????????????????????
               3900 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667725 ????????????????????????????????????????????????????????????
               3960 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667785 ????????????????????????????????????????????????????????????
               4020 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667845 ????????????????????????????????????????????????????????????
               4080 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667905 ????????????????????????????????????????????????????????????
               4140 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48667965 ????????????????????????????????????????????????????????????
               4200 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668025 ????????????????????????????????????????????????????????????
               4260 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668085 ????????????????????????????????????????????????????????????
               4320 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668145 ????????????????????????????????????????????????????????????
               4380 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668205 ????????????????????????????????????????????????????????????
               4440 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668265 ????????????????????????????????????????????????????????????
               4500 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668325 ????????????????????????????????????????????????????????????
               4560 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668385 ????????????????????????????????????????????????????????????
               4620 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668445 ????????????????????????????????????????????????????????????
               4680 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668505 ????????????????????????????????????????????????????????????
               4740 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668565 ????????????????????????????????????????????????????????????
               4800 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668625 ????????????????????????????????????????????????????????????
               4860 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668685 ????????????????????????????????????????????????????????????
               4920 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668745 ????????????????????????????????????????????????????????????
               4980 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668805 ????????????????????????????????????????????????????????????
               5040 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668865 ????????????????????????????????????????????????????????????
               5100 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668925 ????????????????????????????????????????????????????????????
               5160 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48668985 ????????????????????????????????????????????????????????????
               5220 ------------------------------------------------------------
NR_111921       132 ------------------------------------------------------------

chr3       48669045 ?????????????????????????????????????????????????????AGACGGG
               5280 -----------------------------------------------------|||||||
NR_111921       132 -----------------------------------------------------AGACGGG

chr3       48669105 AGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTAT
               5340 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NR_111921       139 AGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTAT

chr3       48669165 ATTAAAAAA 48669174
               5400 |||||||||     5409
NR_111921       199 ATTAAAAAA      208
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
NR_111921.1_modified	0	chr3	48663768	0	3S28M1D17M1827N76M2I6M3376N76M12H	*	0	0	AAACACGAGAGGAGCGGAGGCGAGGGGTGAAGCGGAGCACTCCAATCGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGCTGCTGCCCGGCAGATGGAGCGATCAGAAGCCACCAGGAGACGGGAGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATATTAAAAAA	*	AS:i:972	NM:i:5
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (203 aligned letters; 201 identities; 2 mismatches; 5206 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 203:
        identities = 201,
        mismatches = 2.
    gaps = 5206:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 5206:
            internal_insertions = 2:
                open_internal_insertions = 1,
                extend_internal_insertions = 1;
            internal_deletions = 5204:
                open_internal_deletions = 3,
                extend_internal_deletions = 5201;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 2)
        self.assertEqual(counts.internal_deletions, 5204)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 5206)
        self.assertEqual(counts.insertions, 2)
        self.assertEqual(counts.deletions, 5204)
        self.assertEqual(counts.gaps, 5206)
        self.assertEqual(counts.aligned, 203)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading(self):
        """Test parsing dna_rna.sam."""
        path = "Blat/dna_rna.sam"
        alignments = Align.parse(path, "sam")
        self.check_alignments(alignments)
        alignments = iter(alignments)
        self.check_alignments(alignments)
        with Align.parse(path, "sam") as alignments:
            self.check_alignments(alignments)
        with self.assertRaises(AttributeError):
            alignments._stream
        with Align.parse(path, "sam") as alignments:
            pass
        with self.assertRaises(AttributeError):
            alignments._stream

    def test_reading_psl_comparison(self):
        """Test parsing dna_rna.sam and comparing to dna_rna.psl."""
        path = "Blat/dna_rna.sam"
        sam_alignments = Align.parse(path, "sam")
        path = "Blat/dna_rna.psl"
        psl_alignments = Align.parse(path, "psl")
        for sam_alignment, psl_alignment in zip(sam_alignments, psl_alignments):
            self.assertEqual(sam_alignment.target.id, psl_alignment.target.id)
            self.assertEqual(sam_alignment.query.id, psl_alignment.query.id)
            self.assertTrue(
                np.array_equal(sam_alignment.coordinates, psl_alignment.coordinates)
            )

    def test_writing(self):
        """Test writing the alignments in dna_rna.sam."""
        path = "Blat/dna_rna.sam"
        alignments = Align.parse(path, "sam")
        stream = StringIO()
        n = Align.write(alignments, stream, "sam", md=True)
        self.assertEqual(n, 4)
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        self.check_alignments(alignments)
        stream.close()


class TestAlign_dna(unittest.TestCase):
    # The SAM files were generated using these commands:
    # twoBitInfo hg19.2bit stdout | grep -v chrUn | grep -v _random | grep -v _hap |  sort -n -k 2 -r > hg19.chrom.sizes

    # psl2sam.pl psl_34_001.psl | samtools view -h -t hg19.chrom.sizes - > psl_34_001.sam
    # psl2sam.pl psl_34_003.psl | samtools view -h -t hg19.chrom.sizes - > psl_34_003.sam
    # psl2sam.pl psl_34_004.psl | samtools view -h -t hg19.chrom.sizes - > psl_34_004.sam
    # psl2sam.pl psl_34_005.psl | samtools view -h -t hg19.chrom.sizes - > psl_34_005.sam

    # Note that psl_34_002 was not included as the SAM format no longer allows
    # an empty SAM file.

    # The hard clipping symbols H were replaced by soft clipping symbols S in
    # the file psl_34_005.sam.

    def check_alignments_psl_34_001(self, alignments):
        """Check the alignments for psl_34_001/sam."""
        self.assertEqual(list(alignments.metadata), ["PG"])
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1]), 243199373)
        self.assertEqual(alignments.targets[2].id, "chr3")
        self.assertEqual(len(alignments.targets[2]), 198022430)
        self.assertEqual(alignments.targets[3].id, "chr4")
        self.assertEqual(len(alignments.targets[3]), 191154276)
        self.assertEqual(alignments.targets[4].id, "chr5")
        self.assertEqual(len(alignments.targets[4]), 180915260)
        self.assertEqual(alignments.targets[5].id, "chr6")
        self.assertEqual(len(alignments.targets[5]), 171115067)
        self.assertEqual(alignments.targets[6].id, "chr7")
        self.assertEqual(len(alignments.targets[6]), 159138663)
        self.assertEqual(alignments.targets[7].id, "chrX")
        self.assertEqual(len(alignments.targets[7]), 155270560)
        self.assertEqual(alignments.targets[8].id, "chr8")
        self.assertEqual(len(alignments.targets[8]), 146364022)
        self.assertEqual(alignments.targets[9].id, "chr9")
        self.assertEqual(len(alignments.targets[9]), 141213431)
        self.assertEqual(alignments.targets[10].id, "chr10")
        self.assertEqual(len(alignments.targets[10]), 135534747)
        self.assertEqual(alignments.targets[11].id, "chr11")
        self.assertEqual(len(alignments.targets[11]), 135006516)
        self.assertEqual(alignments.targets[12].id, "chr12")
        self.assertEqual(len(alignments.targets[12]), 133851895)
        self.assertEqual(alignments.targets[13].id, "chr13")
        self.assertEqual(len(alignments.targets[13]), 115169878)
        self.assertEqual(alignments.targets[14].id, "chr14")
        self.assertEqual(len(alignments.targets[14]), 107349540)
        self.assertEqual(alignments.targets[15].id, "chr15")
        self.assertEqual(len(alignments.targets[15]), 102531392)
        self.assertEqual(alignments.targets[16].id, "chr16")
        self.assertEqual(len(alignments.targets[16]), 90354753)
        self.assertEqual(alignments.targets[17].id, "chr17")
        self.assertEqual(len(alignments.targets[17]), 81195210)
        self.assertEqual(alignments.targets[18].id, "chr18")
        self.assertEqual(len(alignments.targets[18]), 78077248)
        self.assertEqual(alignments.targets[19].id, "chr20")
        self.assertEqual(len(alignments.targets[19]), 63025520)
        self.assertEqual(alignments.targets[20].id, "chrY")
        self.assertEqual(len(alignments.targets[20]), 59373566)
        self.assertEqual(alignments.targets[21].id, "chr19")
        self.assertEqual(len(alignments.targets[21]), 59128983)
        self.assertEqual(alignments.targets[22].id, "chr22")
        self.assertEqual(len(alignments.targets[22]), 51304566)
        self.assertEqual(alignments.targets[23].id, "chr21")
        self.assertEqual(len(alignments.targets[23]), 48129895)
        self.assertEqual(alignments.targets[24].id, "chrM")
        self.assertEqual(len(alignments.targets[24]), 16571)
        self.assertEqual(len(alignments.metadata["PG"]), 1)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "samtools",
                "PN": "samtools",
                "VN": "1.14",
                "CL": "samtools view -h -t hg19.chrom.sizes -",
            },
        )
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 16))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 16)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [       0,       16]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       61646095 ???????????????? 61646111
                  0 ||||||||||||||||       16
hg18_dna          0 ????????????????       16
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr4	61646096	0	11H16M6H	*	0	0	*	*	AS:i:16
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 16:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 16)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 33))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 33)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       10271783 ????????????????????????????????? 10271816
                  0 |||||||||||||||||||||||||||||||||       33
hg18_dna          0 ?????????????????????????????????       33
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr1	10271784	0	33M	*	0	0	*	*	AS:i:33
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 33:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 33)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 17))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 17)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      17,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2       53575980 ????????????????? 53575997
                  0 |||||||||||||||||       17
hg18_dna         17 ?????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	16	chr2	53575981	0	8H17M8H	*	0	0	*	*	AS:i:17
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 17:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 17)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr9")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 141213431)
        self.assertEqual(len(alignment.query.seq), 41)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       0,       41]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr9       85737865 ????????????????????????????????????????? 85737906
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          0 ?????????????????????????????????????????       41
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr9	85737866	0	9H41M	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr8")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 146364022)
        self.assertEqual(len(alignment.query.seq), 41)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       0,       41]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr8       95160479 ????????????????????????????????????????? 95160520
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          0 ?????????????????????????????????????????       41
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr8	95160480	0	8H41M1H	*	0	0	*	*	AS:i:41
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [       0,       36]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      42144400 ???????????????????????????????????? 42144436
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna          0 ????????????????????????????????????       36
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr22	42144401	0	11H36M3H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 48)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183925990, 183926028],
                          [        0,         6,        10,        48]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      183925984 ??????----?????????????????????????????????????? 183926028
                  0 ||||||----||||||||||||||||||||||||||||||||||||||        48
hg19_dna          0 ????????????????????????????????????????????????        48
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr2	183925985	0	1H6M4I38M1H	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 170))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [       0,       25,       25,       36]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      35483340 ????????????????????????????????????????????????????????????
                  0 |||||||||||||||||||||||||-----------------------------------
hg19_dna          0 ?????????????????????????-----------------------------------

chr19      35483400 ????????????????????????????????????????????????????????????
                 60 ------------------------------------------------------------
hg19_dna         25 ------------------------------------------------------------

chr19      35483460 ?????????????????????????????????????????????????? 35483510
                120 ---------------------------------------|||||||||||      170
hg19_dna         25 ---------------------------------------???????????       36
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr19	35483341	0	10H25M134D11M4H	*	0	0	*	*	AS:i:0
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 134:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 134:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 134:
                open_internal_deletions = 1,
                extend_internal_deletions = 133;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 134)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 134)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 134)
        self.assertEqual(counts.gaps, 134)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [       0,       39]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      23891310 ??????????????????????????????????????? 23891349
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna          0 ???????????????????????????????????????       39
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	23891311	0	10H39M1H	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 28))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 28)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [       0,       28]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      43252217 ???????????????????????????? 43252245
                  0 ||||||||||||||||||||||||||||       28
hg19_dna          0 ????????????????????????????       28
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	43252218	0	21H28M1H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 51))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr13")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 115169878)
        self.assertEqual(len(alignment.query.seq), 48)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759157, 52759160, 52759198],
                          [       0,       10,       10,       48]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr13      52759147 ??????????????????????????????????????????????????? 52759198
                  0 ||||||||||---||||||||||||||||||||||||||||||||||||||       51
hg19_dna          0 ??????????---??????????????????????????????????????       48
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr13	52759148	0	1H10M3D38M1H	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (48 aligned letters; 0 identities; 0 mismatches; 3 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 48:
        identities = 0,
        mismatches = 0.
    gaps = 3:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 3:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 3:
                open_internal_deletions = 1,
                extend_internal_deletions = 2;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 3)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 3)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 3)
        self.assertEqual(counts.gaps, 3)
        self.assertEqual(counts.aligned, 48)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 50))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1        1207056 ?????????????????????????????????????????????????? 1207106
                  0 ||||||||||||||||||||||||||||||||||||||||||||||||||      50
hg19_dna          0 ??????????????????????????????????????????????????      50
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	1207057	0	50M	*	0	0	*	*	AS:i:50
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 50:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 50)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 34)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       0,       34]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       61700837 ?????????????????????????????????? 61700871
                  0 ||||||||||||||||||||||||||||||||||       34
hg19_dna          0 ??????????????????????????????????       34
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	61700838	0	1H34M15H	*	0	0	*	*	AS:i:22
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 38))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 38)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558173, 37558173, 37558191],
                          [      38,       22,       18,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       37558157 ????????????????----?????????????????? 37558191
                  0 ||||||||||||||||----||||||||||||||||||       38
hg19_dna         38 ??????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr4	37558158	0	1H16M4I18M11H	*	0	0	*	*	AS:i:15
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 37)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      37,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      48997405 ????????????????????????????????????? 48997442
                  0 |||||||||||||||||||||||||||||||||||||       37
hg19_dna         37 ?????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr22	48997406	0	1H37M12H	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 37:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 37)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       36,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      120641740 ???????????????????????????????????? 120641776
                  0 ||||||||||||||||||||||||||||||||||||        36
hg19_dna         36 ????????????????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr2	120641741	0	1H36M13H	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      39,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      54017130 ??????????????????????????????????????? 54017169
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna         39 ???????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	54017131	0	1H39M10H	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    39,      0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19        553742 ??????????????????????????????????????? 553781
                  0 |||||||||||||||||||||||||||||||||||||||     39
hg19_dna         39 ???????????????????????????????????????      0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	553743	0	1H39M10H	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      36,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10      99388555 ???????????????????????????????????? 99388591
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         36 ????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	99388556	0	1H36M13H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 25))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 25)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       25,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10     112178171 ????????????????????????? 112178196
                  0 |||||||||||||||||||||||||        25
hg19_dna         25 ?????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	112178172	0	15H25M10H	*	0	0	*	*	AS:i:21
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 25:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 25)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                          [      36,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       39368490 ???????????????????????????????????? 39368526
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         36 ????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	39368491	0	1H36M13H	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 34)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       34,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1      220325687 ?????????????????????????????????? 220325721
                  0 ||||||||||||||||||||||||||||||||||        34
hg19_dna         34 ??????????????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	220325688	0	3H34M13H	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_001(self):
        """Test parsing psl_34_001.sam."""
        path = "Blat/psl_34_001.sam"
        alignments = Align.parse(path, "sam")
        self.check_alignments_psl_34_001(alignments)

    def test_writing_psl_34_001(self):
        """Test writing the alignments in psl_34_001.sam."""
        path = "Blat/psl_34_001.sam"
        alignments = Align.parse(path, "sam")
        stream = StringIO()
        n = Align.write(alignments, stream, "sam")
        self.assertEqual(n, 22)
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        self.check_alignments_psl_34_001(alignments)
        stream.close()

    def check_alignments_psl_34_003(self, alignments):
        """Check the alignments for psl_34_003/sam."""
        self.assertEqual(list(alignments.metadata), ["PG"])
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1]), 243199373)
        self.assertEqual(alignments.targets[2].id, "chr3")
        self.assertEqual(len(alignments.targets[2]), 198022430)
        self.assertEqual(alignments.targets[3].id, "chr4")
        self.assertEqual(len(alignments.targets[3]), 191154276)
        self.assertEqual(alignments.targets[4].id, "chr5")
        self.assertEqual(len(alignments.targets[4]), 180915260)
        self.assertEqual(alignments.targets[5].id, "chr6")
        self.assertEqual(len(alignments.targets[5]), 171115067)
        self.assertEqual(alignments.targets[6].id, "chr7")
        self.assertEqual(len(alignments.targets[6]), 159138663)
        self.assertEqual(alignments.targets[7].id, "chrX")
        self.assertEqual(len(alignments.targets[7]), 155270560)
        self.assertEqual(alignments.targets[8].id, "chr8")
        self.assertEqual(len(alignments.targets[8]), 146364022)
        self.assertEqual(alignments.targets[9].id, "chr9")
        self.assertEqual(len(alignments.targets[9]), 141213431)
        self.assertEqual(alignments.targets[10].id, "chr10")
        self.assertEqual(len(alignments.targets[10]), 135534747)
        self.assertEqual(alignments.targets[11].id, "chr11")
        self.assertEqual(len(alignments.targets[11]), 135006516)
        self.assertEqual(alignments.targets[12].id, "chr12")
        self.assertEqual(len(alignments.targets[12]), 133851895)
        self.assertEqual(alignments.targets[13].id, "chr13")
        self.assertEqual(len(alignments.targets[13]), 115169878)
        self.assertEqual(alignments.targets[14].id, "chr14")
        self.assertEqual(len(alignments.targets[14]), 107349540)
        self.assertEqual(alignments.targets[15].id, "chr15")
        self.assertEqual(len(alignments.targets[15]), 102531392)
        self.assertEqual(alignments.targets[16].id, "chr16")
        self.assertEqual(len(alignments.targets[16]), 90354753)
        self.assertEqual(alignments.targets[17].id, "chr17")
        self.assertEqual(len(alignments.targets[17]), 81195210)
        self.assertEqual(alignments.targets[18].id, "chr18")
        self.assertEqual(len(alignments.targets[18]), 78077248)
        self.assertEqual(alignments.targets[19].id, "chr20")
        self.assertEqual(len(alignments.targets[19]), 63025520)
        self.assertEqual(alignments.targets[20].id, "chrY")
        self.assertEqual(len(alignments.targets[20]), 59373566)
        self.assertEqual(alignments.targets[21].id, "chr19")
        self.assertEqual(len(alignments.targets[21]), 59128983)
        self.assertEqual(alignments.targets[22].id, "chr22")
        self.assertEqual(len(alignments.targets[22]), 51304566)
        self.assertEqual(alignments.targets[23].id, "chr21")
        self.assertEqual(len(alignments.targets[23]), 48129895)
        self.assertEqual(alignments.targets[24].id, "chrM")
        self.assertEqual(len(alignments.targets[24]), 16571)
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(len(alignments.metadata["PG"]), 1)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "samtools",
                "PN": "samtools",
                "VN": "1.14",
                "CL": "samtools view -h -t hg19.chrom.sizes -",
            },
        )
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 16))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 16)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [       0,       16]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       61646095 ???????????????? 61646111
                  0 ||||||||||||||||       16
hg18_dna          0 ????????????????       16
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr4	61646096	0	11H16M6H	*	0	0	*	*	AS:i:16
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 16:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 16)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 33))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 33)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       10271783 ????????????????????????????????? 10271816
                  0 |||||||||||||||||||||||||||||||||       33
hg18_dna          0 ?????????????????????????????????       33
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr1	10271784	0	33M	*	0	0	*	*	AS:i:33
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 33:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 33)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 17))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 17)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      17,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2       53575980 ????????????????? 53575997
                  0 |||||||||||||||||       17
hg18_dna         17 ?????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	16	chr2	53575981	0	8H17M8H	*	0	0	*	*	AS:i:17
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 17:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 17)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_003(self):
        """Test parsing psl_34_003.sam."""
        path = "Blat/psl_34_003.sam"
        alignments = Align.parse(path, "sam")
        self.check_alignments_psl_34_003(alignments)

    def test_writing_psl_34_003(self):
        """Test writing the alignments in psl_34_003.sam."""
        path = "Blat/psl_34_003.sam"
        alignments = Align.parse(path, "sam")
        stream = StringIO()
        n = Align.write(alignments, stream, "sam")
        self.assertEqual(n, 3)
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        self.check_alignments_psl_34_003(alignments)
        stream.close()

    def check_alignments_psl_34_004(self, alignments):
        """Check the alignments for psl_34_004/sam."""
        self.assertEqual(list(alignments.metadata), ["PG"])
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1]), 243199373)
        self.assertEqual(alignments.targets[2].id, "chr3")
        self.assertEqual(len(alignments.targets[2]), 198022430)
        self.assertEqual(alignments.targets[3].id, "chr4")
        self.assertEqual(len(alignments.targets[3]), 191154276)
        self.assertEqual(alignments.targets[4].id, "chr5")
        self.assertEqual(len(alignments.targets[4]), 180915260)
        self.assertEqual(alignments.targets[5].id, "chr6")
        self.assertEqual(len(alignments.targets[5]), 171115067)
        self.assertEqual(alignments.targets[6].id, "chr7")
        self.assertEqual(len(alignments.targets[6]), 159138663)
        self.assertEqual(alignments.targets[7].id, "chrX")
        self.assertEqual(len(alignments.targets[7]), 155270560)
        self.assertEqual(alignments.targets[8].id, "chr8")
        self.assertEqual(len(alignments.targets[8]), 146364022)
        self.assertEqual(alignments.targets[9].id, "chr9")
        self.assertEqual(len(alignments.targets[9]), 141213431)
        self.assertEqual(alignments.targets[10].id, "chr10")
        self.assertEqual(len(alignments.targets[10]), 135534747)
        self.assertEqual(alignments.targets[11].id, "chr11")
        self.assertEqual(len(alignments.targets[11]), 135006516)
        self.assertEqual(alignments.targets[12].id, "chr12")
        self.assertEqual(len(alignments.targets[12]), 133851895)
        self.assertEqual(alignments.targets[13].id, "chr13")
        self.assertEqual(len(alignments.targets[13]), 115169878)
        self.assertEqual(alignments.targets[14].id, "chr14")
        self.assertEqual(len(alignments.targets[14]), 107349540)
        self.assertEqual(alignments.targets[15].id, "chr15")
        self.assertEqual(len(alignments.targets[15]), 102531392)
        self.assertEqual(alignments.targets[16].id, "chr16")
        self.assertEqual(len(alignments.targets[16]), 90354753)
        self.assertEqual(alignments.targets[17].id, "chr17")
        self.assertEqual(len(alignments.targets[17]), 81195210)
        self.assertEqual(alignments.targets[18].id, "chr18")
        self.assertEqual(len(alignments.targets[18]), 78077248)
        self.assertEqual(alignments.targets[19].id, "chr20")
        self.assertEqual(len(alignments.targets[19]), 63025520)
        self.assertEqual(alignments.targets[20].id, "chrY")
        self.assertEqual(len(alignments.targets[20]), 59373566)
        self.assertEqual(alignments.targets[21].id, "chr19")
        self.assertEqual(len(alignments.targets[21]), 59128983)
        self.assertEqual(alignments.targets[22].id, "chr22")
        self.assertEqual(len(alignments.targets[22]), 51304566)
        self.assertEqual(alignments.targets[23].id, "chr21")
        self.assertEqual(len(alignments.targets[23]), 48129895)
        self.assertEqual(alignments.targets[24].id, "chrM")
        self.assertEqual(len(alignments.targets[24]), 16571)
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(len(alignments.metadata["PG"]), 1)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "samtools",
                "PN": "samtools",
                "VN": "1.14",
                "CL": "samtools view -h -t hg19.chrom.sizes -",
            },
        )
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr9")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 141213431)
        self.assertEqual(len(alignment.query.seq), 41)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       0,       41]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr9       85737865 ????????????????????????????????????????? 85737906
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          0 ?????????????????????????????????????????       41
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr9	85737866	0	9H41M	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr8")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 146364022)
        self.assertEqual(len(alignment.query.seq), 41)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       0,       41]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr8       95160479 ????????????????????????????????????????? 95160520
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          0 ?????????????????????????????????????????       41
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr8	95160480	0	8H41M1H	*	0	0	*	*	AS:i:41
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [       0,       36]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      42144400 ???????????????????????????????????? 42144436
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna          0 ????????????????????????????????????       36
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr22	42144401	0	11H36M3H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 48))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 48)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183925990, 183926028],
                          [        0,         6,        10,        48]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      183925984 ??????----?????????????????????????????????????? 183926028
                  0 ||||||----||||||||||||||||||||||||||||||||||||||        48
hg19_dna          0 ????????????????????????????????????????????????        48
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr2	183925985	0	1H6M4I38M1H	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 170))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [       0,       25,       25,       36]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      35483340 ????????????????????????????????????????????????????????????
                  0 |||||||||||||||||||||||||-----------------------------------
hg19_dna          0 ?????????????????????????-----------------------------------

chr19      35483400 ????????????????????????????????????????????????????????????
                 60 ------------------------------------------------------------
hg19_dna         25 ------------------------------------------------------------

chr19      35483460 ?????????????????????????????????????????????????? 35483510
                120 ---------------------------------------|||||||||||      170
hg19_dna         25 ---------------------------------------???????????       36
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr19	35483341	0	10H25M134D11M4H	*	0	0	*	*	AS:i:0
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 134:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 134:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 134:
                open_internal_deletions = 1,
                extend_internal_deletions = 133;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 134)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 134)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 134)
        self.assertEqual(counts.gaps, 134)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [       0,       39]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      23891310 ??????????????????????????????????????? 23891349
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna          0 ???????????????????????????????????????       39
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	23891311	0	10H39M1H	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 28))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 28)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [       0,       28]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      43252217 ???????????????????????????? 43252245
                  0 ||||||||||||||||||||||||||||       28
hg19_dna          0 ????????????????????????????       28
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	43252218	0	21H28M1H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 51))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr13")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 115169878)
        self.assertEqual(len(alignment.query.seq), 48)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759157, 52759160, 52759198],
                          [       0,       10,       10,       48]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr13      52759147 ??????????????????????????????????????????????????? 52759198
                  0 ||||||||||---||||||||||||||||||||||||||||||||||||||       51
hg19_dna          0 ??????????---??????????????????????????????????????       48
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr13	52759148	0	1H10M3D38M1H	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (48 aligned letters; 0 identities; 0 mismatches; 3 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 48:
        identities = 0,
        mismatches = 0.
    gaps = 3:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 3:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 3:
                open_internal_deletions = 1,
                extend_internal_deletions = 2;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 3)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 3)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 3)
        self.assertEqual(counts.gaps, 3)
        self.assertEqual(counts.aligned, 48)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 50))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1        1207056 ?????????????????????????????????????????????????? 1207106
                  0 ||||||||||||||||||||||||||||||||||||||||||||||||||      50
hg19_dna          0 ??????????????????????????????????????????????????      50
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	1207057	0	50M	*	0	0	*	*	AS:i:50
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 50:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 50)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 34)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       0,       34]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       61700837 ?????????????????????????????????? 61700871
                  0 ||||||||||||||||||||||||||||||||||       34
hg19_dna          0 ??????????????????????????????????       34
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	61700838	0	1H34M15H	*	0	0	*	*	AS:i:22
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 38))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 38)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558173, 37558173, 37558191],
                          [      38,       22,       18,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       37558157 ????????????????----?????????????????? 37558191
                  0 ||||||||||||||||----||||||||||||||||||       38
hg19_dna         38 ??????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr4	37558158	0	1H16M4I18M11H	*	0	0	*	*	AS:i:15
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 37))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 37)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      37,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      48997405 ????????????????????????????????????? 48997442
                  0 |||||||||||||||||||||||||||||||||||||       37
hg19_dna         37 ?????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr22	48997406	0	1H37M12H	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 37:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 37)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       36,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      120641740 ???????????????????????????????????? 120641776
                  0 ||||||||||||||||||||||||||||||||||||        36
hg19_dna         36 ????????????????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr2	120641741	0	1H36M13H	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      39,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      54017130 ??????????????????????????????????????? 54017169
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna         39 ???????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	54017131	0	1H39M10H	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 39)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    39,      0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19        553742 ??????????????????????????????????????? 553781
                  0 |||||||||||||||||||||||||||||||||||||||     39
hg19_dna         39 ???????????????????????????????????????      0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	553743	0	1H39M10H	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      36,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10      99388555 ???????????????????????????????????? 99388591
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         36 ????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	99388556	0	1H36M13H	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 25))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 25)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       25,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10     112178171 ????????????????????????? 112178196
                  0 |||||||||||||||||||||||||        25
hg19_dna         25 ?????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	112178172	0	15H25M10H	*	0	0	*	*	AS:i:21
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 25:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 25)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 36)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                          [      36,        0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       39368490 ???????????????????????????????????? 39368526
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         36 ????????????????????????????????????        0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	39368491	0	1H36M13H	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 34)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       34,         0]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1      220325687 ?????????????????????????????????? 220325721
                  0 ||||||||||||||||||||||||||||||||||        34
hg19_dna         34 ??????????????????????????????????         0
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	220325688	0	3H34M13H	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_004(self):
        """Test parsing psl_34_004.sam."""
        path = "Blat/psl_34_004.sam"
        alignments = Align.parse(path, "sam")
        self.check_alignments_psl_34_004(alignments)

    def test_writing_psl_34_004(self):
        """Test writing the alignments in psl_34_004.sam."""
        path = "Blat/psl_34_004.sam"
        alignments = Align.parse(path, "sam")
        stream = StringIO()
        n = Align.write(alignments, stream, "sam")
        self.assertEqual(n, 19)
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        self.check_alignments_psl_34_004(alignments)
        stream.close()

    def check_alignments_psl_34_005(self, alignments):
        """Check the alignments for psl_34_005.sam."""
        self.assertEqual(list(alignments.metadata), ["PG"])
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1]), 243199373)
        self.assertEqual(alignments.targets[2].id, "chr3")
        self.assertEqual(len(alignments.targets[2]), 198022430)
        self.assertEqual(alignments.targets[3].id, "chr4")
        self.assertEqual(len(alignments.targets[3]), 191154276)
        self.assertEqual(alignments.targets[4].id, "chr5")
        self.assertEqual(len(alignments.targets[4]), 180915260)
        self.assertEqual(alignments.targets[5].id, "chr6")
        self.assertEqual(len(alignments.targets[5]), 171115067)
        self.assertEqual(alignments.targets[6].id, "chr7")
        self.assertEqual(len(alignments.targets[6]), 159138663)
        self.assertEqual(alignments.targets[7].id, "chrX")
        self.assertEqual(len(alignments.targets[7]), 155270560)
        self.assertEqual(alignments.targets[8].id, "chr8")
        self.assertEqual(len(alignments.targets[8]), 146364022)
        self.assertEqual(alignments.targets[9].id, "chr9")
        self.assertEqual(len(alignments.targets[9]), 141213431)
        self.assertEqual(alignments.targets[10].id, "chr10")
        self.assertEqual(len(alignments.targets[10]), 135534747)
        self.assertEqual(alignments.targets[11].id, "chr11")
        self.assertEqual(len(alignments.targets[11]), 135006516)
        self.assertEqual(alignments.targets[12].id, "chr12")
        self.assertEqual(len(alignments.targets[12]), 133851895)
        self.assertEqual(alignments.targets[13].id, "chr13")
        self.assertEqual(len(alignments.targets[13]), 115169878)
        self.assertEqual(alignments.targets[14].id, "chr14")
        self.assertEqual(len(alignments.targets[14]), 107349540)
        self.assertEqual(alignments.targets[15].id, "chr15")
        self.assertEqual(len(alignments.targets[15]), 102531392)
        self.assertEqual(alignments.targets[16].id, "chr16")
        self.assertEqual(len(alignments.targets[16]), 90354753)
        self.assertEqual(alignments.targets[17].id, "chr17")
        self.assertEqual(len(alignments.targets[17]), 81195210)
        self.assertEqual(alignments.targets[18].id, "chr18")
        self.assertEqual(len(alignments.targets[18]), 78077248)
        self.assertEqual(alignments.targets[19].id, "chr20")
        self.assertEqual(len(alignments.targets[19]), 63025520)
        self.assertEqual(alignments.targets[20].id, "chrY")
        self.assertEqual(len(alignments.targets[20]), 59373566)
        self.assertEqual(alignments.targets[21].id, "chr19")
        self.assertEqual(len(alignments.targets[21]), 59128983)
        self.assertEqual(alignments.targets[22].id, "chr22")
        self.assertEqual(len(alignments.targets[22]), 51304566)
        self.assertEqual(alignments.targets[23].id, "chr21")
        self.assertEqual(len(alignments.targets[23]), 48129895)
        self.assertEqual(alignments.targets[24].id, "chrM")
        self.assertEqual(len(alignments.targets[24]), 16571)
        self.assertEqual(len(alignments.targets), 25)
        self.assertEqual(len(alignments.metadata["PG"]), 1)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "samtools",
                "PN": "samtools",
                "VN": "1.14",
                "CL": "samtools view -h -t hg19.chrom.sizes -",
            },
        )
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 16))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 33)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [      11,       27]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       61646095 ???????????????? 61646111
                  0 ||||||||||||||||       16
hg18_dna         11 ????????????????       27
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr4	61646096	0	11S16M6S	*	0	0	*	*	AS:i:16
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 16:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 16)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 33))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 33)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       10271783 ????????????????????????????????? 10271816
                  0 |||||||||||||||||||||||||||||||||       33
hg18_dna          0 ?????????????????????????????????       33
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	0	chr1	10271784	0	33M	*	0	0	*	*	AS:i:33
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 33:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 33)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 17))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg18_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 33)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      25,        8]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2       53575980 ????????????????? 53575997
                  0 |||||||||||||||||       17
hg18_dna         25 ?????????????????        8
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg18_dna	16	chr2	53575981	0	8S17M8S	*	0	0	*	*	AS:i:17
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 17:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 17)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr9")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 141213431)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       9,       50]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr9       85737865 ????????????????????????????????????????? 85737906
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          9 ?????????????????????????????????????????       50
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr9	85737866	0	9S41M	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 41))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr8")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 146364022)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       8,       49]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr8       95160479 ????????????????????????????????????????? 95160520
                  0 |||||||||||||||||||||||||||||||||||||||||       41
hg19_dna          8 ?????????????????????????????????????????       49
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr8	95160480	0	8S41M1S	*	0	0	*	*	AS:i:41
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 41:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 41)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [      11,       47]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      42144400 ???????????????????????????????????? 42144436
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         11 ????????????????????????????????????       47
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr22	42144401	0	11S36M3S	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 48))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183925990, 183926028],
                          [        1,         7,        11,        49]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      183925984 ??????----?????????????????????????????????????? 183926028
                  0 ||||||----||||||||||||||||||||||||||||||||||||||        48
hg19_dna          1 ????????????????????????????????????????????????        49
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr2	183925985	0	1S6M4I38M1S	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 170))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [      10,       35,       35,       46]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      35483340 ????????????????????????????????????????????????????????????
                  0 |||||||||||||||||||||||||-----------------------------------
hg19_dna         10 ?????????????????????????-----------------------------------

chr19      35483400 ????????????????????????????????????????????????????????????
                 60 ------------------------------------------------------------
hg19_dna         35 ------------------------------------------------------------

chr19      35483460 ?????????????????????????????????????????????????? 35483510
                120 ---------------------------------------|||||||||||      170
hg19_dna         35 ---------------------------------------???????????       46
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr19	35483341	0	10S25M134D11M4S	*	0	0	*	*	AS:i:0
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 134:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 134:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 134:
                open_internal_deletions = 1,
                extend_internal_deletions = 133;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 134)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 134)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 134)
        self.assertEqual(counts.gaps, 134)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [      10,       49]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      23891310 ??????????????????????????????????????? 23891349
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna         10 ???????????????????????????????????????       49
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	23891311	0	10S39M1S	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 28))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr18")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 78077248)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [      21,       49]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr18      43252217 ???????????????????????????? 43252245
                  0 ||||||||||||||||||||||||||||       28
hg19_dna         21 ????????????????????????????       49
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr18	43252218	0	21S28M1S	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 51))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr13")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 115169878)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759157, 52759160, 52759198],
                          [       1,       11,       11,       49]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr13      52759147 ??????????????????????????????????????????????????? 52759198
                  0 ||||||||||---||||||||||||||||||||||||||||||||||||||       51
hg19_dna          1 ??????????---??????????????????????????????????????       49
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr13	52759148	0	1S10M3D38M1S	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (48 aligned letters; 0 identities; 0 mismatches; 3 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 48:
        identities = 0,
        mismatches = 0.
    gaps = 3:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 3:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 3:
                open_internal_deletions = 1,
                extend_internal_deletions = 2;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 3)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 3)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 3)
        self.assertEqual(counts.gaps, 3)
        self.assertEqual(counts.aligned, 48)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 50))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1        1207056 ?????????????????????????????????????????????????? 1207106
                  0 ||||||||||||||||||||||||||||||||||||||||||||||||||      50
hg19_dna          0 ??????????????????????????????????????????????????      50
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	1207057	0	50M	*	0	0	*	*	AS:i:50
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 50:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 50)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       1,       35]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       61700837 ?????????????????????????????????? 61700871
                  0 ||||||||||||||||||||||||||||||||||       34
hg19_dna          1 ??????????????????????????????????       35
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	0	chr1	61700838	0	1S34M15S	*	0	0	*	*	AS:i:22
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 38))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 191154276)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558173, 37558173, 37558191],
                          [      49,       33,       29,       11]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr4       37558157 ????????????????----?????????????????? 37558191
                  0 ||||||||||||||||----||||||||||||||||||       38
hg19_dna         49 ??????????????????????????????????????       11
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr4	37558158	0	1S16M4I18M11S	*	0	0	*	*	AS:i:15
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 4:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 4:
            internal_insertions = 4:
                open_internal_insertions = 1,
                extend_internal_insertions = 3;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 4)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 4)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 4)
        self.assertEqual(counts.aligned, 34)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 37))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr22")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 51304566)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      49,       12]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr22      48997405 ????????????????????????????????????? 48997442
                  0 |||||||||||||||||||||||||||||||||||||       37
hg19_dna         49 ?????????????????????????????????????       12
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr22	48997406	0	1S37M12S	*	0	0	*	*	AS:i:29
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 37:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 37)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr2")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 243199373)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       49,        13]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr2      120641740 ???????????????????????????????????? 120641776
                  0 ||||||||||||||||||||||||||||||||||||        36
hg19_dna         49 ????????????????????????????????????        13
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr2	120641741	0	1S36M13S	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      49,       10]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19      54017130 ??????????????????????????????????????? 54017169
                  0 |||||||||||||||||||||||||||||||||||||||       39
hg19_dna         49 ???????????????????????????????????????       10
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	54017131	0	1S39M10S	*	0	0	*	*	AS:i:39
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 39))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr19")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 59128983)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    49,     10]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr19        553742 ??????????????????????????????????????? 553781
                  0 |||||||||||||||||||||||||||||||||||||||     39
hg19_dna         49 ???????????????????????????????????????     10
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr19	553743	0	1S39M10S	*	0	0	*	*	AS:i:27
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 39:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      49,       13]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10      99388555 ???????????????????????????????????? 99388591
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         49 ????????????????????????????????????       13
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	99388556	0	1S36M13S	*	0	0	*	*	AS:i:24
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 25))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr10")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 135534747)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       35,        10]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr10     112178171 ????????????????????????? 112178196
                  0 |||||||||||||||||||||||||        25
hg19_dna         35 ?????????????????????????        10
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr10	112178172	0	15S25M10S	*	0	0	*	*	AS:i:21
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 25:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 25)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 36))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                             [      49,       13]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1       39368490 ???????????????????????????????????? 39368526
                  0 ||||||||||||||||||||||||||||||||||||       36
hg19_dna         49 ????????????????????????????????????       13
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	39368491	0	1S36M13S	*	0	0	*	*	AS:i:32
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 36:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 36)
        alignment = next(alignments)
        self.assertEqual(alignment.shape, (2, 34))
        self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
        self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
        self.assertEqual(len(alignment), 2)
        self.assertIs(alignment.sequences[0], alignment.target)
        self.assertIs(alignment.sequences[1], alignment.query)
        self.assertEqual(alignment.target.id, "chr1")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertEqual(len(alignment.target.seq), 249250621)
        self.assertEqual(len(alignment.query.seq), 50)
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       47,        13]]),
                # fmt: on
            )
        )
        self.assertEqual(
            str(alignment),
            """\
chr1      220325687 ?????????????????????????????????? 220325721
                  0 ||||||||||||||||||||||||||||||||||        34
hg19_dna         47 ??????????????????????????????????        13
""",
        )
        self.assertEqual(
            format(alignment, "sam"),
            """\
hg19_dna	16	chr1	220325688	0	3S34M13S	*	0	0	*	*	AS:i:30
""",
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 34:
        identities = 0,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 34)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_005(self):
        """Test parsing psl_34_005.sam."""
        path = "Blat/psl_34_005.sam"
        alignments = Align.parse(path, "sam")
        self.check_alignments_psl_34_005(alignments)

    def test_writing_psl_34_005(self):
        """Test writing the alignments in psl_34_005.sam."""
        path = "Blat/psl_34_005.sam"
        alignments = Align.parse(path, "sam")
        stream = StringIO()
        n = Align.write(alignments, stream, "sam")
        self.assertEqual(n, 22)
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        self.check_alignments_psl_34_005(alignments)
        stream.close()


class TestAlign_sambam(unittest.TestCase):
    def test_ex1(self):
        alignments = Align.parse("SamBam/ex1.sam", "sam")
        n = 0
        for alignment in alignments:
            n += 1
        self.assertEqual(n, 3270)
        self.assertEqual(alignment.sequences[0].id, "chr2")
        self.assertEqual(alignment.sequences[1].id, "EAS114_26:7:37:79:581")
        self.assertEqual(
            alignment.sequences[1].seq, "TTTTCTGGCATGAAAAAAAAAAAAAAAAAAAAAAA"
        )
        self.assertEqual(alignment.flag, 83)
        self.assertEqual(alignment.mapq, 68)
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[1532, 1567], [35, 0]]))
        )
        self.assertEqual(alignment.rnext, "chr2")
        self.assertEqual(alignment.pnext, 1348)
        self.assertEqual(alignment.tlen, -219)
        self.assertEqual(
            alignment.sequences[1].letter_annotations["phred_quality"],
            [
                18,
                11,
                11,
                11,
                28,
                28,
                28,
                21,
                28,
                28,
                28,
                27,
                28,
                28,
                28,
                27,
                26,
                28,
                28,
                28,
                28,
                28,
                12,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
            ],
        )
        self.assertEqual(len(alignment.annotations), 6)
        self.assertEqual(alignment.annotations["MF"], 18)
        self.assertEqual(alignment.annotations["Aq"], 27)
        self.assertEqual(alignment.annotations["NM"], 2)
        self.assertEqual(alignment.annotations["UQ"], 23)
        self.assertEqual(alignment.annotations["H0"], 0)
        self.assertEqual(alignment.annotations["H1"], 1)

    def test_ex1_header(self):
        alignments = Align.parse("SamBam/ex1_header.sam", "sam")
        self.assertEqual(alignments.metadata["HD"], {"VN": "1.3", "SO": "coordinate"})
        self.assertEqual(len(alignments.targets), 2)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0].seq), 1575)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1].seq), 1584)
        n = 0
        for alignment in alignments:
            n += 1
        self.assertEqual(n, 3270)
        self.assertEqual(alignment.sequences[0].id, "chr2")
        self.assertEqual(len(alignment.sequences[0].seq), 1584)
        self.assertEqual(alignment.sequences[1].id, "EAS114_26:7:37:79:581")
        self.assertEqual(
            alignment.sequences[1].seq, "TTTTCTGGCATGAAAAAAAAAAAAAAAAAAAAAAA"
        )
        self.assertEqual(alignment.flag, 83)
        self.assertEqual(alignment.mapq, 68)
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[1532, 1567], [35, 0]]))
        )
        self.assertEqual(alignment.rnext, "chr2")
        self.assertEqual(alignment.pnext, 1348)
        self.assertEqual(alignment.tlen, -219)
        self.assertEqual(
            alignment.sequences[1].letter_annotations["phred_quality"],
            [
                18,
                11,
                11,
                11,
                28,
                28,
                28,
                21,
                28,
                28,
                28,
                27,
                28,
                28,
                28,
                27,
                26,
                28,
                28,
                28,
                28,
                28,
                12,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
                28,
            ],
        )
        self.assertEqual(len(alignment.annotations), 6)
        self.assertEqual(alignment.annotations["MF"], 18)
        self.assertEqual(alignment.annotations["Aq"], 27)
        self.assertEqual(alignment.annotations["NM"], 2)
        self.assertEqual(alignment.annotations["UQ"], 23)
        self.assertEqual(alignment.annotations["H0"], 0)
        self.assertEqual(alignment.annotations["H1"], 1)

    def test_sam1(self):
        alignments = Align.parse("SamBam/sam1.sam", "sam")
        self.assertEqual(len(alignments.targets), 1)
        self.assertEqual(alignments.targets[0].id, "1")
        self.assertEqual(len(alignments.targets[0].seq), 239940)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "bwa",
                "PN": "bwa",
                "VN": "0.6.2-r126",
            },
        )
        n = 0
        for alignment in alignments:
            n += 1
        self.assertEqual(n, 200)
        self.assertIsNone(alignment.sequences[0])
        self.assertEqual(
            alignment.sequences[1].id, "HWI-1KL120:88:D0LRBACXX:1:1101:5516:2195"
        )
        self.assertEqual(
            alignment.sequences[1].seq,
            "GGCCCAACCGTCCTATATGAGATGTAGCATGGTACAGAACAAACTGCTTACACAGGTCTCACTAGTTAGAAACCTGTGGGCCATGGAGGTCAGACATCCAT",
        )
        self.assertEqual(alignment.flag, 141)
        self.assertEqual(alignment.mapq, 0)
        self.assertIsNone(alignment.coordinates)
        self.assertEqual(
            alignment.sequences[1].letter_annotations["phred_quality"],
            [
                33,
                30,
                16,
                32,
                35,
                35,
                35,
                35,
                32,
                37,
                37,
                37,
                35,
                36,
                38,
                37,
                36,
                38,
                39,
                36,
                36,
                35,
                30,
                35,
                30,
                36,
                33,
                27,
                36,
                38,
                33,
                26,
                37,
                29,
                37,
                39,
                40,
                29,
                38,
                36,
                33,
                39,
                36,
                37,
                31,
                31,
                27,
                33,
                37,
                29,
                35,
                30,
                37,
                27,
                37,
                33,
                28,
                34,
                29,
                37,
                26,
                34,
                31,
                37,
                34,
                22,
                31,
                28,
                26,
                28,
                36,
                28,
                22,
                28,
                30,
                31,
                26,
                26,
                26,
                23,
                20,
                21,
                30,
                31,
                26,
                26,
                26,
                26,
                20,
                20,
                24,
                7,
                11,
                11,
                20,
                30,
                18,
                29,
                20,
                29,
                31,
            ],
        )

    def test_sam2(self):
        alignments = Align.parse("SamBam/sam2.sam", "sam")
        self.assertEqual(len(alignments.targets), 1)
        self.assertEqual(alignments.targets[0].id, "1")
        self.assertEqual(len(alignments.targets[0].seq), 239940)
        self.assertEqual(
            alignments.metadata["PG"][0],
            {
                "ID": "bwa",
                "PN": "bwa",
                "VN": "0.6.2-r126",
            },
        )
        n = 0
        for alignment in alignments:
            if n == 8:
                self.assertEqual(alignment.sequences[0].id, "1")
                self.assertEqual(len(alignment.sequences[0].seq), 239940)
                self.assertEqual(
                    alignment.sequences[0].seq.defined_ranges, ((132615, 132716),)
                )
                self.assertEqual(
                    alignment.sequences[0].seq[132615:132716],
                    "GGTCACACCCTGTCCTCCTCCTACACATACTCGGATGCTTCCTCCTCAACCTTGGCACCCACCTCCTTCTTACTGGGCCCAGGAGCCTTCAAAGCCCAGGA",
                )
                self.assertEqual(
                    alignment.sequences[1].id,
                    "HWI-1KL120:88:D0LRBACXX:1:1101:2205:2204",
                )
                self.assertEqual(
                    alignment.sequences[1].seq,
                    "TCCTGGGCATTGAAGGCTCCTGGGCCCAGTAAGAAGGAGGTGGGTGCCAAGGTTGAGGAGGAAGCATCCGAGTATGTGTAGGAGGAGGACAAGGTGGGACC",
                )
                self.assertEqual(alignment.flag, 83)
                self.assertEqual(alignment.mapq, 60)
                self.assertTrue(
                    np.array_equal(
                        alignment.coordinates, np.array([[132615, 132716], [101, 0]])
                    )
                )
                self.assertEqual(alignment.rnext, "1")
                self.assertEqual(alignment.pnext, 132490)
                self.assertEqual(alignment.tlen, -226)
                self.assertEqual(
                    alignment.sequences[1].letter_annotations["phred_quality"],
                    [
                        33,
                        33,
                        33,
                        31,
                        30,
                        34,
                        29,
                        30,
                        30,
                        30,
                        34,
                        33,
                        33,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        34,
                        34,
                        29,
                        34,
                        29,
                        29,
                        34,
                        30,
                        30,
                        30,
                        28,
                        35,
                        36,
                        36,
                        36,
                        35,
                        37,
                        36,
                        35,
                        33,
                        38,
                        38,
                        39,
                        40,
                        40,
                        36,
                        36,
                        35,
                        28,
                        39,
                        37,
                        32,
                        38,
                        40,
                        40,
                        39,
                        35,
                        39,
                        38,
                        35,
                        30,
                        38,
                        40,
                        41,
                        41,
                        41,
                        40,
                        39,
                        40,
                        38,
                        37,
                        35,
                        39,
                        37,
                        40,
                        41,
                        41,
                        41,
                        40,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        39,
                        39,
                        39,
                        39,
                        37,
                        37,
                        37,
                        37,
                        37,
                        37,
                        34,
                        34,
                        34,
                    ],
                )
                self.assertEqual(len(alignment.annotations), 9)
                self.assertEqual(alignment.annotations["XT"], "U")
                self.assertEqual(alignment.annotations["NM"], 3)
                self.assertEqual(alignment.annotations["SM"], 37)
                self.assertEqual(alignment.annotations["AM"], 37)
                self.assertEqual(alignment.annotations["X0"], 1)
                self.assertEqual(alignment.annotations["X1"], 0)
                self.assertEqual(alignment.annotations["XM"], 3)
                self.assertEqual(alignment.annotations["XO"], 0)
                self.assertEqual(alignment.annotations["XG"], 0)
            elif n == 9:
                self.assertEqual(alignment.sequences[0].id, "1")
                self.assertEqual(len(alignment.sequences[0].seq), 239940)
                self.assertEqual(
                    alignment.sequences[0].seq.defined_ranges, ((132490, 132591),)
                )
                self.assertEqual(
                    alignment.sequences[0].seq[132490:132591],
                    "GCAACAAGGGCTTTGGTGGGAAGGTATTTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCGCCCCTTGCTGGATCCTGAGCCCCCAGGGTCCCCCGATC",
                )
                self.assertEqual(
                    alignment.sequences[1].id,
                    "HWI-1KL120:88:D0LRBACXX:1:1101:2205:2204",
                )
                self.assertEqual(
                    alignment.sequences[1].seq,
                    "GCAACAAGGGCTTTGGTGGGAAGGTATCTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCGCCCCTTGCTGGATCCTGAGCCCCCAGGGTCCCCCGATC",
                )
                self.assertEqual(alignment.flag, 163)
                self.assertEqual(alignment.mapq, 60)
                self.assertTrue(
                    np.array_equal(
                        alignment.coordinates, np.array([[132490, 132591], [0, 101]])
                    )
                )
                self.assertEqual(alignment.rnext, "1")
                self.assertEqual(alignment.pnext, 132615)
                self.assertEqual(alignment.tlen, 226)
                self.assertEqual(
                    alignment.sequences[1].letter_annotations["phred_quality"],
                    [
                        34,
                        34,
                        34,
                        35,
                        37,
                        37,
                        37,
                        37,
                        39,
                        39,
                        39,
                        39,
                        39,
                        41,
                        41,
                        39,
                        36,
                        39,
                        40,
                        41,
                        40,
                        40,
                        40,
                        41,
                        30,
                        36,
                        39,
                        40,
                        41,
                        40,
                        40,
                        41,
                        41,
                        41,
                        38,
                        39,
                        37,
                        38,
                        34,
                        39,
                        38,
                        41,
                        41,
                        40,
                        40,
                        40,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        39,
                        40,
                        40,
                        40,
                        40,
                        40,
                        41,
                        41,
                        41,
                        41,
                        40,
                        41,
                        39,
                        37,
                        37,
                        33,
                        36,
                        34,
                        36,
                        36,
                        35,
                        35,
                        33,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        29,
                        31,
                        27,
                        20,
                        24,
                        32,
                        33,
                        35,
                        35,
                        33,
                        33,
                        2,
                        2,
                        2,
                    ],
                )
                self.assertEqual(len(alignment.annotations), 9)
                self.assertEqual(alignment.annotations["XT"], "U")
                self.assertEqual(alignment.annotations["NM"], 1)
                self.assertEqual(alignment.annotations["SM"], 37)
                self.assertEqual(alignment.annotations["AM"], 37)
                self.assertEqual(alignment.annotations["X0"], 1)
                self.assertEqual(alignment.annotations["X1"], 0)
                self.assertEqual(alignment.annotations["XM"], 1)
                self.assertEqual(alignment.annotations["XO"], 0)
                self.assertEqual(alignment.annotations["XG"], 0)
            elif n == 100:
                self.assertEqual(alignment.sequences[0].id, "1")
                self.assertEqual(len(alignment.sequences[0].seq), 239940)
                self.assertEqual(
                    alignment.sequences[0].seq.defined_ranges, ((137538, 137639),)
                )
                self.assertEqual(
                    alignment.sequences[0].seq[137538:137639],
                    "AAAGTTCGGGGCCTACAAAGGCGGTTGGGAGCTGGGCAGGAGTTGAGCCAAAAGAGCTTGCTTACTTGCTGGGAGGCAGGGCCGGGAGAGCCCGACTTCAG",
                )
                self.assertEqual(
                    alignment.sequences[1].id,
                    "HWI-1KL120:88:D0LRBACXX:1:1101:4673:2125",
                )
                self.assertEqual(
                    alignment.sequences[1].seq,
                    "AAAGTTCGGGGCCTACAAAGGCGGTTGGGAGCTGGGCAGGAGTTGAGCCAAAAGAGCTTGCTTACTTGCTGGGAGGCAGGACCGGGAGAGGCCGACTTCAG",
                )
                self.assertEqual(alignment.flag, 97)
                self.assertEqual(alignment.mapq, 37)
                self.assertTrue(
                    np.array_equal(
                        alignment.coordinates, np.array([[137538, 137639], [0, 101]])
                    )
                )
                self.assertEqual(alignment.rnext, "1")
                self.assertEqual(alignment.pnext, 135649)
                self.assertEqual(alignment.tlen, -1788)
                self.assertEqual(
                    alignment.sequences[1].letter_annotations["phred_quality"],
                    [
                        34,
                        34,
                        34,
                        37,
                        37,
                        37,
                        37,
                        37,
                        39,
                        39,
                        39,
                        39,
                        39,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        38,
                        39,
                        38,
                        40,
                        41,
                        40,
                        40,
                        40,
                        41,
                        41,
                        40,
                        41,
                        40,
                        39,
                        39,
                        39,
                        37,
                        37,
                        34,
                        34,
                        34,
                        36,
                        36,
                        34,
                        36,
                        36,
                        35,
                        35,
                        33,
                        35,
                        35,
                        35,
                        34,
                        35,
                        35,
                        35,
                        34,
                        35,
                        34,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        30,
                        33,
                        31,
                        33,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        35,
                        33,
                        35,
                        35,
                        35,
                        33,
                        29,
                        31,
                        35,
                        33,
                        31,
                        34,
                        34,
                        35,
                    ],
                )
                self.assertEqual(len(alignment.annotations), 9)
                self.assertEqual(alignment.annotations["XT"], "U")
                self.assertEqual(alignment.annotations["NM"], 2)
                self.assertEqual(alignment.annotations["SM"], 37)
                self.assertEqual(alignment.annotations["AM"], 37)
                self.assertEqual(alignment.annotations["X0"], 1)
                self.assertEqual(alignment.annotations["X1"], 0)
                self.assertEqual(alignment.annotations["XM"], 2)
                self.assertEqual(alignment.annotations["XO"], 0)
                self.assertEqual(alignment.annotations["XG"], 0)
            elif n == 101:
                self.assertEqual(alignment.sequences[0].id, "1")
                self.assertEqual(len(alignment.sequences[0].seq), 239940)
                self.assertEqual(
                    alignment.sequences[0].seq.defined_ranges, ((135649, 135750),)
                )
                self.assertEqual(
                    alignment.sequences[0].seq[135649:135750],
                    "TGGAGAGGCCACCGCGAGGCCTGAGCTGGGCCTGGGGAGCTTGGCTTAGGGAAGTTGTGGGCCTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCA",
                )
                self.assertEqual(
                    alignment.sequences[1].id,
                    "HWI-1KL120:88:D0LRBACXX:1:1101:4673:2125",
                )
                self.assertEqual(
                    alignment.sequences[1].seq,
                    "TGGACTCAGCTCCTGCCCAGCTCCCAGCGGCCCTGGTAGGCCCACAACTTCCCGAAGCCAAGCTCCCCAGGCCCAGCTCAGGCCTCACGGTGGCCTCTCCA",
                )
                self.assertEqual(alignment.flag, 145)
                self.assertEqual(alignment.mapq, 37)
                self.assertTrue(
                    np.array_equal(
                        alignment.coordinates, np.array([[135649, 135750], [101, 0]])
                    )
                )
                self.assertEqual(alignment.rnext, "1")
                self.assertEqual(alignment.pnext, 137538)
                self.assertEqual(alignment.tlen, 1788)
                self.assertEqual(
                    alignment.sequences[1].letter_annotations["phred_quality"],
                    [
                        34,
                        34,
                        34,
                        32,
                        33,
                        34,
                        32,
                        32,
                        33,
                        33,
                        31,
                        33,
                        33,
                        35,
                        35,
                        35,
                        35,
                        33,
                        35,
                        34,
                        35,
                        34,
                        35,
                        35,
                        33,
                        35,
                        35,
                        35,
                        35,
                        35,
                        33,
                        30,
                        35,
                        35,
                        35,
                        35,
                        35,
                        34,
                        33,
                        35,
                        36,
                        34,
                        36,
                        35,
                        37,
                        37,
                        39,
                        37,
                        39,
                        40,
                        40,
                        41,
                        41,
                        40,
                        41,
                        41,
                        41,
                        40,
                        41,
                        41,
                        40,
                        40,
                        39,
                        39,
                        38,
                        41,
                        40,
                        41,
                        40,
                        41,
                        40,
                        41,
                        40,
                        38,
                        41,
                        41,
                        41,
                        41,
                        41,
                        41,
                        40,
                        41,
                        40,
                        40,
                        41,
                        41,
                        41,
                        41,
                        39,
                        39,
                        39,
                        39,
                        39,
                        37,
                        37,
                        37,
                        37,
                        37,
                        34,
                        34,
                        34,
                    ],
                )
                self.assertEqual(len(alignment.annotations), 9)
                self.assertEqual(alignment.annotations["XT"], "U")
                self.assertEqual(alignment.annotations["NM"], 2)
                self.assertEqual(alignment.annotations["SM"], 37)
                self.assertEqual(alignment.annotations["AM"], 37)
                self.assertEqual(alignment.annotations["X0"], 1)
                self.assertEqual(alignment.annotations["X1"], 0)
                self.assertEqual(alignment.annotations["XM"], 2)
                self.assertEqual(alignment.annotations["XO"], 0)
                self.assertEqual(alignment.annotations["XG"], 0)
            else:
                self.assertIsNone(alignment.sequences[0])
                self.assertEqual(alignment.mapq, 0)
                self.assertIsNone(alignment.coordinates)
            n += 1
        self.assertEqual(n, 200)


class TestAlign_tlen(unittest.TestCase):
    def test_preserve_tlen(self):
        """Test writing an explicit TLEN value."""
        target = SeqRecord(Seq("N" * 100), id="target")
        query = SeqRecord(Seq("ATGCATGCAT"), id="read")
        coordinates = np.array([[10, 20], [0, 10]])
        alignment = Alignment([target, query], coordinates)
        alignment.flag = 99
        alignment.rnext = "target"
        alignment.pnext = 30
        alignment.tlen = 30
        self.assertEqual(
            alignment.format("sam"),
            "read\t99\ttarget\t11\t255\t10M\t=\t31\t30\tATGCATGCAT\t*\n",
        )

    def test_calculate_tlen(self):
        """Test calculating TLEN for paired alignments."""
        target = SeqRecord(Seq("N" * 100), id="target")
        query1 = SeqRecord(Seq("ATGCATGCAT"), id="read")
        query2 = SeqRecord(Seq("ATGCATGCAT"), id="read")
        coordinates1 = np.array([[10, 20], [0, 10]])
        coordinates2 = np.array([[30, 40], [10, 0]])
        alignment1 = Alignment([target, query1], coordinates1)
        alignment1.flag = 99
        alignment1.rnext = "target"
        alignment1.pnext = 30
        alignment2 = Alignment([target, query2], coordinates2)
        alignment2.flag = 147
        alignment2.rnext = "target"
        alignment2.pnext = 10
        stream = StringIO()
        n = Align.write([alignment1, alignment2], stream, "sam")
        self.assertEqual(n, 2)
        self.assertEqual(
            stream.getvalue(),
            "read\t99\ttarget\t11\t255\t10M\t=\t31\t30\tATGCATGCAT\t*\n"
            "read\t147\ttarget\t31\t255\t10M\t=\t11\t-30\tATGCATGCAT\t*\n",
        )
        stream.seek(0)
        alignments = Align.parse(stream, "sam")
        alignment1 = next(alignments)
        alignment2 = next(alignments)
        self.assertEqual(alignment1.tlen, 30)
        self.assertEqual(alignment2.tlen, -30)


class TestAlign_clipping(unittest.TestCase):
    def test_6M(self):
        """Test alignment starting at non-zero position."""
        target_seq = Seq("AAAAAAAACCCCCC")
        query_seq = Seq("CCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[8, 14], [0, 6]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            8 CCCCCC 14
                  0 ||||||  6
query             0 CCCCCC  6
""",
        )
        line = alignment.format("sam")
        self.assertEqual(line, "query\t0\ttarget\t9\t255\t6M\t*\t0\t0\tCCCCCC\t*\n")
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 8)
        cigar = fields[5]
        self.assertEqual(cigar, "6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['C', 'C', 'C', 'C', 'C', 'C'],
          ['C', 'C', 'C', 'C', 'C', 'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_8D6M_ex1(self):
        """Test alignment starting with deletion."""
        target_seq = Seq("AAAAAAAACCCCCC")
        query_seq = Seq("CCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 8, 14], [0, 0, 6]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 AAAAAAAACCCCCC 14
                  0 --------|||||| 14
query             0 --------CCCCCC  6
""",
        )
        line = alignment.format("sam")
        self.assertEqual(line, "query\t0\ttarget\t1\t255\t8D6M\t*\t0\t0\tCCCCCC\t*\n")
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "8D6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 8:
                open_left_deletions = 1,
                extend_left_deletions = 7;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 8)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 8)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_8D6M_ex2(self):
        """Test alignment starting with deletion at non-zero position."""
        target_seq = Seq("GGGGAAAAAAAACCCCCC")
        query_seq = Seq("CCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[4, 12, 18], [0, 0, 6]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            4 AAAAAAAACCCCCC 18
                  0 --------|||||| 14
query             0 --------CCCCCC  6
""",
        )
        line = alignment.format("sam")
        self.assertEqual(line, "query\t0\ttarget\t5\t255\t8D6M\t*\t0\t0\tCCCCCC\t*\n")
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 4)
        cigar = fields[5]
        self.assertEqual(cigar, "8D6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 8:
                open_left_deletions = 1,
                extend_left_deletions = 7;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 8)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 8)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_8I6M_ex1(self):
        """Test alignment starting with insertion."""
        target_seq = Seq("CCCCCC")
        query_seq = Seq("AAAAAAAACCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 0, 6], [0, 8, 14]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 --------CCCCCC  6
                  0 --------|||||| 14
query             0 AAAAAAAACCCCCC 14
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t8I6M\t*\t0\t0\tAAAAAAAACCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "8I6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 8:
                open_left_insertions = 1,
                extend_left_insertions = 7;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 8)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 8)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_8I6M_ex2(self):
        """Test alignment starting with insertion at non-zero position."""
        target_seq = Seq("GGGGCCCCCC")
        query_seq = Seq("AAAAAAAACCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[4, 4, 10], [0, 8, 14]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            4 --------CCCCCC 10
                  0 --------|||||| 14
query             0 AAAAAAAACCCCCC 14
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t5\t255\t8I6M\t*\t0\t0\tAAAAAAAACCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 4)
        cigar = fields[5]
        self.assertEqual(cigar, "8I6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 8:
                open_left_insertions = 1,
                extend_left_insertions = 7;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 8)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 8)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_8S6M(self):
        """Test alignment starting with soft clip."""
        target_seq = Seq("CCCCCC")
        query_seq = Seq("AAAAAAAACCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 6], [8, 14]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 CCCCCC  6
                  0 ||||||  6
query             8 CCCCCC 14
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t8S6M\t*\t0\t0\tAAAAAAAACCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "8S6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['C', 'C', 'C', 'C', 'C', 'C'],
          ['C', 'C', 'C', 'C', 'C', 'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_4S8D6M(self):
        """Test alignment starting with soft clip followed by deletion."""
        target_seq = Seq("AAAAAAAACCCCCC")
        query_seq = Seq("GGGGCCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 8, 14], [4, 4, 10]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 AAAAAAAACCCCCC 14
                  0 --------|||||| 14
query             4 --------CCCCCC 10
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t4S8D6M\t*\t0\t0\tGGGGCCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "4S8D6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 8:
                open_left_deletions = 1,
                extend_left_deletions = 7;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 8)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 8)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_4I8D6M(self):
        """Test alignment starting with insertion followed by deletion."""
        target_seq = Seq("AAAAAAAACCCCCC")
        query_seq = Seq("GGGGCCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 0, 8, 14], [0, 4, 4, 10]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 ----AAAAAAAACCCCCC 14
                  0 ------------|||||| 18
query             0 GGGG--------CCCCCC 10
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t4I8D6M\t*\t0\t0\tGGGGCCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "4I8D6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C',
           'C', 'C', 'C', 'C', 'C'],
          ['G', 'G', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', 'C',
           'C', 'C', 'C', 'C', 'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 12 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 12:
        left_gaps = 4:
            left_insertions = 4:
                open_left_insertions = 1,
                extend_left_insertions = 3;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 8:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 8:
                open_internal_deletions = 1,
                extend_internal_deletions = 7;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 4)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 8)
        self.assertEqual(counts.left_gaps, 4)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 8)
        self.assertEqual(counts.insertions, 4)
        self.assertEqual(counts.deletions, 8)
        self.assertEqual(counts.gaps, 12)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_4S6M(self):
        """Test alignment starting with soft clip at non-zero position."""
        target_seq = Seq("AAAAAAAACCCCCC")
        query_seq = Seq("GGGGCCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[8, 14], [4, 10]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            8 CCCCCC 14
                  0 ||||||  6
query             4 CCCCCC 10
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t9\t255\t4S6M\t*\t0\t0\tGGGGCCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 8)
        cigar = fields[5]
        self.assertEqual(cigar, "4S6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['C', 'C', 'C', 'C', 'C', 'C'],
          ['C', 'C', 'C', 'C', 'C', 'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 0:
        left_gaps = 0:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 0)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_4D8I6M(self):
        """Test alignment starting with deletion followed by insertion."""
        target_seq = Seq("GGGGCCCCCC")
        query_seq = Seq("AAAAAAAACCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 4, 4, 10], [0, 0, 8, 14]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 GGGG--------CCCCCC 10
                  0 ------------|||||| 18
query             0 ----AAAAAAAACCCCCC 14
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t4D8I6M\t*\t0\t0\tAAAAAAAACCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "4D8I6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['G', 'G', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', 'C',
           'C', 'C', 'C', 'C', 'C'],
          ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C',
           'C', 'C', 'C', 'C', 'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 12 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 12:
        left_gaps = 4:
            left_insertions = 0:
                open_left_insertions = 0,
                extend_left_insertions = 0;
            left_deletions = 4:
                open_left_deletions = 1,
                extend_left_deletions = 3;
        internal_gaps = 8:
            internal_insertions = 8:
                open_internal_insertions = 1,
                extend_internal_insertions = 7;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 0)
        self.assertEqual(counts.left_deletions, 4)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 8)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 4)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 8)
        self.assertEqual(counts.insertions, 8)
        self.assertEqual(counts.deletions, 4)
        self.assertEqual(counts.gaps, 12)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))

    def test_4S8I6M(self):
        """Test alignment starting with soft clip followed by insertion."""
        target_seq = Seq("CCCCCC")
        query_seq = Seq("GGGGAAAAAAAACCCCCC")
        target = SeqRecord(target_seq, id="target")
        query = SeqRecord(query_seq, id="query")
        sequences = [target, query]
        coordinates = np.array([[0, 0, 6], [4, 12, 18]])
        alignment = Alignment(sequences, coordinates)
        self.assertEqual(
            str(alignment),
            """\
target            0 --------CCCCCC  6
                  0 --------|||||| 14
query             4 AAAAAAAACCCCCC 18
""",
        )
        line = alignment.format("sam")
        self.assertEqual(
            line, "query\t0\ttarget\t1\t255\t4S8I6M\t*\t0\t0\tGGGGAAAAAAAACCCCCC\t*\n"
        )
        fields = line.split()
        pos = int(fields[3]) - 1
        self.assertEqual(pos, 0)
        cigar = fields[5]
        self.assertEqual(cigar, "4S8I6M")
        stream = StringIO(line)
        alignments = Align.parse(stream, "sam")
        self.assertTrue(
            np.array_equal(
                np.array(alignment, "U"),
                # fmt: off
np.array([['-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'C', 'C',
           'C'],
          ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C',
           'C']], dtype='U')
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (6 aligned letters; 6 identities; 0 mismatches; 8 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 6:
        identities = 6,
        mismatches = 0.
    gaps = 8:
        left_gaps = 8:
            left_insertions = 8:
                open_left_insertions = 1,
                extend_left_insertions = 7;
            left_deletions = 0:
                open_left_deletions = 0,
                extend_left_deletions = 0;
        internal_gaps = 0:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 0:
                open_internal_deletions = 0,
                extend_internal_deletions = 0;
        right_gaps = 0:
            right_insertions = 0:
                open_right_insertions = 0,
                extend_right_insertions = 0;
            right_deletions = 0:
                open_right_deletions = 0,
                extend_right_deletions = 0.
""",
        )
        self.assertEqual(counts.left_insertions, 8)
        self.assertEqual(counts.left_deletions, 0)
        self.assertEqual(counts.right_insertions, 0)
        self.assertEqual(counts.right_deletions, 0)
        self.assertEqual(counts.internal_insertions, 0)
        self.assertEqual(counts.internal_deletions, 0)
        self.assertEqual(counts.left_gaps, 8)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 0)
        self.assertEqual(counts.insertions, 8)
        self.assertEqual(counts.deletions, 0)
        self.assertEqual(counts.gaps, 8)
        self.assertEqual(counts.aligned, 6)
        self.assertEqual(counts.identities, 6)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        stream.close()
        self.assertTrue(np.array_equal(alignment.coordinates, coordinates))


class TestAlign_strand(unittest.TestCase):
    def test_format(self):
        """Test alignment with the target on the opposite strand."""
        sequences = ["AACAGCAGCGTGTCG", "CAGCTAGCGAA"]
        coordinates = np.array(
            [[0, 2, 2, 3, 4, 6, 6, 9, 10, 12, 15], [11, 11, 9, 8, 8, 6, 5, 2, 2, 0, 0]]
        )
        alignment = Alignment(sequences, coordinates)
        alignment.score = 8
        line = """\
query	16	target	1	255	2D2I1M1D2M1I3M1D2M3D	*	0	0	TTCGCTAGCTG	*	AS:i:8
"""
        self.assertEqual(
            str(alignment),
            """\
target            0 AA--CAGC-AGCGTGTCG 15
                  0 ----|-||-|||-||--- 18
query            11 --TTC-GCTAGC-TG---  0
""",
        )
        self.assertEqual(format(alignment, "sam"), line)
        alignment.coordinates = alignment.coordinates[:, ::-1]
        self.assertEqual(
            str(alignment),
            """\
target           15 CGACACGCT-GCTG--TT  0
                  0 ---||-|||-||-|---- 18
query             0 ---CA-GCTAGC-GAA-- 11
""",
        )
        self.assertEqual(format(alignment, "sam"), line)
        alignment.coordinates = alignment.coordinates[:, ::-1]
        line = """\
query	16	target	1	255	3D2M1D3M1I2M1D1M2I2D	*	0	0	CAGCTAGCGAA	*
"""
        alignment = alignment.reverse_complement()
        self.assertEqual(
            str(alignment),
            """\
target            0 CGACACGCT-GCTG--TT 15
                  0 ---||-|||-||-|---- 18
query            11 ---CA-GCTAGC-GAA--  0
""",
        )
        self.assertEqual(format(alignment, "sam"), line)
        alignment.coordinates = alignment.coordinates[:, ::-1]
        self.assertEqual(
            str(alignment),
            """\
target           15 AA--CAGC-AGCGTGTCG  0
                  0 ----|-||-|||-||--- 18
query             0 --TTC-GCTAGC-TG--- 11
""",
        )
        self.assertEqual(format(alignment, "sam"), line)


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
