# 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.bigbed module."""
import os
import sys
import tempfile
import unittest
from io import StringIO

from Bio import Align
from Bio import SeqIO
from Bio.Align import bigbed
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.bigbed."
    ) from None


for i, argument in enumerate(sys.argv):
    if argument == "--big":
        big = True
        sys.argv.pop(i)
        break
else:
    big = False


class TestAlign_dna_rna(unittest.TestCase):
    # The bigBed file dna_rna.bb was generated using the commands
    # sort -k1,1 -k2,2n dna_rna.bed > dna_rna.sorted.bed
    # twoBitInfo hg38.2bit hg38.chrom.sizes
    # bedToBigBed dna_rna.sorted.bed hg38.chrom.sizes dna_rna.bb

    path = "Blat/dna_rna.bb"

    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)
            assert len(sequence) == end - start
            data[start] = sequence
        self.dna = Seq(data, length=198295559)  # hg38 chr3
        records = SeqIO.parse("Blat/rna.fa", "fasta")
        self.rna = {record.id: record.seq for record in records}

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

    def test_writing(self):
        """Test writing dna_rna.bb."""
        alignments = Align.parse(self.path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments(alignments)

    def check_alignments(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 1)
        self.assertEqual(alignments.targets[0].id, "chr3")
        self.assertEqual(len(alignments.targets[0]), 198295559)
        self.assertEqual(len(alignments), 4)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42530895, 42530958, 42532020,
                           42532095, 42532563, 42532606],
                          [     181,      118,      118,
                                 43,       43,        0]])
                # fmt: on
            )
        )
        alignment.target.seq = self.dna
        alignment.query.seq = self.rna[alignment.query.id]
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
            np.array([[36.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0., 40.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0., 57.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0.,  0., 42.,  0.,  0.,  0.,  0.],
                      [ 2.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0.,  3.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
                     ])
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
        # The modified RNAs have gaps in their sequence. As this information is
        # not stored in a BED file, we cannot calculate the substitution matrix.
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (181 aligned letters; 175 identities; 6 mismatches; 1530 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 181:
        identities = 175,
        mismatches = 6.
    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)
        self.assertEqual(counts.identities, 175)
        self.assertEqual(counts.mismatches, 6)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 978)
        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_modified")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42530895, 42530922, 42530958, 42532020, 42532037,
                           42532039, 42532095, 42532563, 42532606],
                          [     179,      152,      116,      116,       99,
                                 99,       43,       43,        0]])
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (179 aligned letters; 0 identities; 0 mismatches; 1532 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 179:
        identities = 0,
        mismatches = 0.
    gaps = 1532:
        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 = 1532:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            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, 0)
        self.assertEqual(counts.internal_deletions, 1532)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 1532)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 1532)
        self.assertEqual(counts.gaps, 1532)
        self.assertEqual(counts.aligned, 179)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48663767, 48663813, 48665640,
                           48665722, 48669098, 48669174],
                          [       0,       46,       46,
                                128,      128,      204]])
                # fmt: on
            )
        )
        alignment.target.seq = self.dna
        alignment.query.seq = self.rna[alignment.query.id]
        self.assertTrue(
            np.array_equal(
                alignment.substitutions,
                # fmt: off
            np.array([[53.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0., 35.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0., 50.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0.,  0., 27.,  0.,  0.,  0.,  0.],
                      [ 9.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  7.,  0.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0., 16.,  0.,  0.,  0.,  0.,  0.],
                      [ 0.,  0.,  0.,  7.,  0.,  0.,  0.,  0.],
                     ])
            )
        )
        self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (204 aligned letters; 165 identities; 39 mismatches; 5203 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 204:
        identities = 165,
        mismatches = 39.
    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)
        self.assertEqual(counts.identities, 165)
        self.assertEqual(counts.mismatches, 39)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 972)
        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_modified")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48663767, 48663795, 48663796, 48663813, 48665640,
                           48665716, 48665722, 48669098, 48669174],
                          [       0,       28,       28,       45,       45,
                                121,      127,      127,      203]])
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (203 aligned letters; 0 identities; 0 mismatches; 5204 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 203:
        identities = 0,
        mismatches = 0.
    gaps = 5204:
        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 = 5204:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            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, 0)
        self.assertEqual(counts.internal_deletions, 5204)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 5204)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 5204)
        self.assertEqual(counts.gaps, 5204)
        self.assertEqual(counts.aligned, 203)
        self.assertRaises(StopIteration, next, alignments)


class TestAlign_dna(unittest.TestCase):
    # The bigBed file psl_34_001.bb was generated using the commands
    # sort -k1,1 -k2,2n psl_34_001.bed > psl_34_001.sorted.bed
    # twoBitInfo hg19.2bit hg19.chrom.sizes
    # bedToBigBed psl_34_001.sorted.bed hg19.chrom.sizes psl_34_001.bb

    # The bigBed file psl_34_003.bb was generated using the commands
    # sort -k1,1 -k2,2n psl_34_003.bed > psl_34_003.sorted.bed
    # twoBitInfo hg19.2bit hg19.chrom.sizes
    # bedToBigBed psl_34_003.sorted.bed hg19.chrom.sizes psl_34_003.bb

    # The bigBed file psl_34_004.bb was generated using the commands
    # sort -k1,1 -k2,2n psl_34_004.bed > psl_34_004.sorted.bed
    # twoBitInfo hg19.2bit hg19.chrom.sizes
    # bedToBigBed psl_34_004.sorted.bed hg19.chrom.sizes psl_34_004.bb

    # The bigBed file psl_34_005.bb was generated using the commands
    # sort -k1,1 -k2,2n psl_34_005.bed > psl_34_005.sorted.bed
    # twoBitInfo hg19.2bit hg19.chrom.sizes
    # bedToBigBed psl_34_005.sorted.bed hg19.chrom.sizes psl_34_005.bb

    def check_alignments_psl_34_001(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 10)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr10")
        self.assertEqual(len(alignments.targets[1]), 135534747)
        self.assertEqual(alignments.targets[2].id, "chr13")
        self.assertEqual(len(alignments.targets[2]), 115169878)
        self.assertEqual(alignments.targets[3].id, "chr18")
        self.assertEqual(len(alignments.targets[3]), 78077248)
        self.assertEqual(alignments.targets[4].id, "chr19")
        self.assertEqual(len(alignments.targets[4]), 59128983)
        self.assertEqual(alignments.targets[5].id, "chr2")
        self.assertEqual(len(alignments.targets[5]), 243199373)
        self.assertEqual(alignments.targets[6].id, "chr22")
        self.assertEqual(len(alignments.targets[6]), 51304566)
        self.assertEqual(alignments.targets[7].id, "chr4")
        self.assertEqual(len(alignments.targets[7]), 191154276)
        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(len(alignments), 22)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 824)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       0,       34]]),
                # fmt: on
            )
        )
        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.score, 942)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       34,         0]]),
                # fmt: on
            )
        )
        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.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 920)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       25,         0]]),
                # fmt: on
            )
        )
        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.score, 912)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759154, 52759160, 52759198],
                          [       0,        7,        7,       45]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 45:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 45)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [       0,       39]]),
                # fmt: on
            )
        )
        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.score, 930)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [       0,       28]]),
                # fmt: on
            )
        )
        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.score, 848)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    39,      0]]),
                # fmt: on
            )
        )
        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.score, 890)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [       0,       25,       25,       36]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      39,        0]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      17,        0]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       36,         0]]),
                # fmt: on
            )
        )
        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.score, 682)
        self.assertEqual(alignment.shape, (2, 44))
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183926028],
                          [        0,         6,        44]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        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, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [       0,       36]]),
                # fmt: on
            )
        )
        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.score, 892)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      37,        0]]),
                # fmt: on
            )
        )
        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.score, 572)
        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, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558167, 37558173, 37558191],
                          [      28,       18,       18,        0]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [       0,       16]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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.score, 854)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_001(self):
        """Test reading psl_34_001.bb."""
        path = "Blat/psl_34_001.bb"
        alignments = Align.parse(path, "bigbed")
        self.check_alignments_psl_34_001(alignments)

    def test_writing_psl_34_001(self):
        """Test writing psl_34_001.bb."""
        path = "Blat/psl_34_001.bb"
        alignments = Align.parse(path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments_psl_34_001(alignments)

    def check_alignments_psl_34_003(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 3)
        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, "chr4")
        self.assertEqual(len(alignments.targets[2]), 191154276)
        self.assertEqual(len(alignments), 3)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      17,        0]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [       0,       16]]),
                # fmt: on
            )
        )
        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)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_003(self):
        """Test reading psl_34_003.bb."""
        path = "Blat/psl_34_003.bb"
        alignments = Align.parse(path, "bigbed")
        self.check_alignments_psl_34_003(alignments)

    def test_writing_psl_34_003(self):
        """Test writing psl_34_003.bb."""
        path = "Blat/psl_34_003.bb"
        alignments = Align.parse(path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments_psl_34_003(alignments)

    def check_alignments_psl_34_004(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 10)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr10")
        self.assertEqual(len(alignments.targets[1]), 135534747)
        self.assertEqual(alignments.targets[2].id, "chr13")
        self.assertEqual(len(alignments.targets[2]), 115169878)
        self.assertEqual(alignments.targets[3].id, "chr18")
        self.assertEqual(len(alignments.targets[3]), 78077248)
        self.assertEqual(alignments.targets[4].id, "chr19")
        self.assertEqual(len(alignments.targets[4]), 59128983)
        self.assertEqual(alignments.targets[5].id, "chr2")
        self.assertEqual(len(alignments.targets[5]), 243199373)
        self.assertEqual(alignments.targets[6].id, "chr22")
        self.assertEqual(len(alignments.targets[6]), 51304566)
        self.assertEqual(alignments.targets[7].id, "chr4")
        self.assertEqual(len(alignments.targets[7]), 191154276)
        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(len(alignments), 19)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 824)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       0,       34]]),
                # fmt: on
            )
        )
        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.score, 942)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       34,         0]]),
                # fmt: on
            )
        )
        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.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 920)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       25,         0]]),
                # fmt: on
            )
        )
        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.score, 912)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759154, 52759160, 52759198],
                          [       0,        7,        7,       45]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 45:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 45)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [       0,       39]]),
                # fmt: on
            )
        )
        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.score, 930)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [       0,       28]]),
                # fmt: on
            )
        )
        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.score, 848)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    39,      0]]),
                # fmt: on
            )
        )
        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.score, 890)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [       0,       25,       25,       36]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      39,        0]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       36,         0]]),
                # fmt: on
            )
        )
        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.score, 682)
        self.assertEqual(alignment.shape, (2, 44))
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183926028],
                          [        0,         6,        44]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        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, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [       0,       36]]),
                # fmt: on
            )
        )
        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.score, 892)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      37,        0]]),
                # fmt: on
            )
        )
        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.score, 572)
        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, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558167, 37558173, 37558191],
                          [      28,       18,       18,        0]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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.score, 854)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_004(self):
        """Test reading psl_34_004.bb."""
        path = "Blat/psl_34_004.bb"
        alignments = Align.parse(path, "bigbed")
        self.check_alignments_psl_34_004(alignments)

    def test_writing_psl_34_004(self):
        """Test writing psl_34_004.bb."""
        path = "Blat/psl_34_004.bb"
        alignments = Align.parse(path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments_psl_34_004(alignments)

    def check_alignments_psl_34_005(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 10)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 249250621)
        self.assertEqual(alignments.targets[1].id, "chr10")
        self.assertEqual(len(alignments.targets[1]), 135534747)
        self.assertEqual(alignments.targets[2].id, "chr13")
        self.assertEqual(len(alignments.targets[2]), 115169878)
        self.assertEqual(alignments.targets[3].id, "chr18")
        self.assertEqual(len(alignments.targets[3]), 78077248)
        self.assertEqual(alignments.targets[4].id, "chr19")
        self.assertEqual(len(alignments.targets[4]), 59128983)
        self.assertEqual(alignments.targets[5].id, "chr2")
        self.assertEqual(len(alignments.targets[5]), 243199373)
        self.assertEqual(alignments.targets[6].id, "chr22")
        self.assertEqual(len(alignments.targets[6]), 51304566)
        self.assertEqual(alignments.targets[7].id, "chr4")
        self.assertEqual(len(alignments.targets[7]), 191154276)
        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(len(alignments), 22)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[1207056, 1207106],
                          [      0,      50]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[10271783, 10271816],
                          [       0,       33]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[39368490, 39368526],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 824)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61700837, 61700871],
                          [       0,       34]]),
                # fmt: on
            )
        )
        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.score, 942)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[220325687, 220325721],
                          [       34,         0]]),
                # fmt: on
            )
        )
        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.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[99388555, 99388591],
                          [      36,        0]]),
                # fmt: on
            )
        )
        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.score, 920)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[112178171, 112178196],
                          [       25,         0]]),
                # fmt: on
            )
        )
        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.score, 912)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[52759147, 52759154, 52759160, 52759198],
                          [       0,        7,        7,       45]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 45:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 45)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[23891310, 23891349],
                          [       0,       39]]),
                # fmt: on
            )
        )
        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.score, 930)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[43252217, 43252245],
                          [       0,       28]]),
                # fmt: on
            )
        )
        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.score, 848)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[553742, 553781],
                          [    39,      0]]),
                # fmt: on
            )
        )
        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.score, 890)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[35483340, 35483365, 35483499, 35483510],
                          [       0,       25,       25,       36]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[54017130, 54017169],
                          [      39,        0]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[53575980, 53575997],
                          [      17,        0]]),
                # fmt: on
            )
        )
        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.score, 946)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[120641740, 120641776],
                          [       36,         0]]),
                # fmt: on
            )
        )
        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.score, 682)
        self.assertEqual(alignment.shape, (2, 44))
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[183925984, 183925990, 183926028],
                          [        0,         6,        44]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 44:
        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, 44)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 834)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[42144400, 42144436],
                          [       0,       36]]),
                # fmt: on
            )
        )
        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.score, 892)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[48997405, 48997442],
                          [      37,        0]]),
                # fmt: on
            )
        )
        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.score, 572)
        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, "chr4")
        self.assertEqual(alignment.query.id, "hg19_dna")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[37558157, 37558167, 37558173, 37558191],
                          [      28,       18,       18,        0]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 6 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 28:
        identities = 0,
        mismatches = 0.
    gaps = 6:
        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 = 6:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 6:
                open_internal_deletions = 1,
                extend_internal_deletions = 5;
        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, 6)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 6)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 6)
        self.assertEqual(counts.gaps, 6)
        self.assertEqual(counts.aligned, 28)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[61646095, 61646111],
                          [       0,       16]]),
                # fmt: on
            )
        )
        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.score, 1000)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[95160479, 95160520],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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.score, 854)
        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.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[85737865, 85737906],
                          [       0,       41]]),
                # fmt: on
            )
        )
        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)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_34_005(self):
        """Test reading psl_34_005.bb."""
        path = "Blat/psl_34_005.bb"
        alignments = Align.parse(path, "bigbed")
        self.check_alignments_psl_34_005(alignments)

    def test_writing_psl_34_005(self):
        """Test writing psl_34_005.bb."""
        path = "Blat/psl_34_005.bb"
        alignments = Align.parse(path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments_psl_34_005(alignments)


class TestAlign_dnax_prot(unittest.TestCase):
    # The bigBed file psl_35_001.bb was generated using the commands
    # sort -k1,1 -k2,2n psl_35_001.bed > psl_35_001.sorted.bed
    # twoBitInfo hg38.2bit hg38.chrom.sizes
    # bedToBigBed psl_35_001.sorted.bed hg38.chrom.sizes psl_35_001.bb

    path = "Blat/psl_35_001.bb"

    def check_alignments(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
        )
        self.assertEqual(len(alignments.targets), 2)
        self.assertEqual(alignments.targets[0].id, "chr13")
        self.assertEqual(len(alignments.targets[0]), 114364328)
        self.assertEqual(alignments.targets[1].id, "chr4")
        self.assertEqual(len(alignments.targets[1]), 190214555)
        self.assertEqual(len(alignments), 8)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 986)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75549820, 75549865, 75567225, 75567312],
                          [       0,       45,       45,      132]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (132 aligned letters; 0 identities; 0 mismatches; 17360 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 132:
        identities = 0,
        mismatches = 0.
    gaps = 17360:
        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 = 17360:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 17360:
                open_internal_deletions = 1,
                extend_internal_deletions = 17359;
        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, 17360)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 17360)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 17360)
        self.assertEqual(counts.gaps, 17360)
        self.assertEqual(counts.aligned, 132)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75560749, 75560881],
                          [       0,      132]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (132 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 132:
        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, 132)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75566694, 75566850],
                          [       0,      156]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (156 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 156:
        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, 156)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75569459, 75569507],
                          [       0,       48]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (48 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 48:
        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, 48)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75594914, 75594989],
                          [       0,       75]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (75 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 75:
        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, 75)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1000)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[75604767, 75604827, 75605728, 75605809],
                          [       0,       60,       60,      141]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (141 aligned letters; 0 identities; 0 mismatches; 901 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 141:
        identities = 0,
        mismatches = 0.
    gaps = 901:
        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 = 901:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 901:
                open_internal_deletions = 1,
                extend_internal_deletions = 900;
        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, 901)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 901)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 901)
        self.assertEqual(counts.gaps, 901)
        self.assertEqual(counts.aligned, 141)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 166)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[41257605, 41257731, 41263227, 41263290],
                          [       0,      126,      126,      189]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (189 aligned letters; 0 identities; 0 mismatches; 5496 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 189:
        identities = 0,
        mismatches = 0.
    gaps = 5496:
        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 = 5496:
            internal_insertions = 0:
                open_internal_insertions = 0,
                extend_internal_insertions = 0;
            internal_deletions = 5496:
                open_internal_deletions = 1,
                extend_internal_deletions = 5495;
        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, 5496)
        self.assertEqual(counts.left_gaps, 0)
        self.assertEqual(counts.right_gaps, 0)
        self.assertEqual(counts.internal_gaps, 5496)
        self.assertEqual(counts.insertions, 0)
        self.assertEqual(counts.deletions, 5496)
        self.assertEqual(counts.gaps, 5496)
        self.assertEqual(counts.aligned, 189)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 530)
        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, "CAG33136.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates,
                # fmt: off
                np.array([[41260685, 41260787],
                          [       0,      102]]),
                # fmt: on
            )
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (102 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 102:
        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, 102)
        self.assertRaises(StopIteration, next, alignments)

    def test_reading_psl_35_001(self):
        """Test parsing psl_35_001.bb."""
        alignments = Align.parse(self.path, "bigbed")
        self.check_alignments(alignments)

    def test_writing_psl_35_001(self):
        """Test writing psl_35_001.bb."""
        alignments = Align.parse(self.path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed")
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments(alignments)


class TestAlign_bed12(unittest.TestCase):
    # The bigBed files were generated using the commands
    # twoBitInfo hg19.2bit hg19.chrom.sizes
    # bedToBigBed bed3.bed hg19.chrom.sizes bed3.bb
    # bedToBigBed bed4.bed hg19.chrom.sizes bed4.bb
    # bedToBigBed bed5.bed hg19.chrom.sizes bed5.bb
    # bedToBigBed bed6.bed hg19.chrom.sizes bed6.bb
    # bedToBigBed bed7.bed hg19.chrom.sizes bed7.bb
    # bedToBigBed bed8.bed hg19.chrom.sizes bed8.bb
    # bedToBigBed bed9.bed hg19.chrom.sizes bed9.bb
    # bedToBigBed bed12.bed hg19.chrom.sizes bed12.bb

    def check_autosql(self, declaration, bedN, msg):
        if bedN == 3:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string chrom;         "Reference sequence chromosome or scaffold"
   uint   chromStart;    "Start position in chromosome"
   uint   chromEnd;      "End position in chromosome"
)
""",
                msg=msg,
            )
        elif bedN == 4:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string chrom;         "Reference sequence chromosome or scaffold"
   uint   chromStart;    "Start position in chromosome"
   uint   chromEnd;      "End position in chromosome"
   string name;          "Name of item."
)
""",
                msg=msg,
            )
        elif bedN == 5:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string chrom;         "Reference sequence chromosome or scaffold"
   uint   chromStart;    "Start position in chromosome"
   uint   chromEnd;      "End position in chromosome"
   string name;          "Name of item."
   uint   score;         "Score (0-1000)"
)
""",
                msg=msg,
            )
        elif bedN == 6:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
)
""",
                msg=msg,
            )
        elif bedN == 7:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
   uint    thickStart;    "Start of where display should be thick (start codon)"
)
""",
                msg=msg,
            )
        elif bedN == 8:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
   uint    thickStart;    "Start of where display should be thick (start codon)"
   uint    thickEnd;      "End of where display should be thick (stop codon)"
)
""",
                msg=msg,
            )
        elif bedN == 9:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
   uint    thickStart;    "Start of where display should be thick (start codon)"
   uint    thickEnd;      "End of where display should be thick (stop codon)"
   uint    reserved;      "Used as itemRgb as of 2004-11-22"
)
""",
                msg=msg,
            )
        elif bedN == 12:
            self.assertEqual(
                str(declaration),
                """\
table bed
"Browser Extensible Data"
(
   string          chrom;          "Reference sequence chromosome or scaffold"
   uint            chromStart;     "Start position in chromosome"
   uint            chromEnd;       "End position in chromosome"
   string          name;           "Name of item."
   uint            score;          "Score (0-1000)"
   char[1]         strand;         "+ or - for strand"
   uint            thickStart;     "Start of where display should be thick (start codon)"
   uint            thickEnd;       "End of where display should be thick (stop codon)"
   uint            reserved;       "Used as itemRgb as of 2004-11-22"
   int             blockCount;     "Number of blocks"
   int[blockCount] blockSizes;     "Comma separated list of block sizes"
   int[blockCount] chromStarts;    "Start positions relative to chromStart"
)
""",
                msg=msg,
            )

    def check_alignments(self, alignments, bedN, msg):
        self.assertEqual(len(alignments), 2)
        alignment = next(alignments)
        if bedN >= 5:
            self.assertEqual(alignment.score, 960, msg=msg)
        self.assertEqual(alignment.shape, (2, 4000), msg=msg)
        self.assertLess(
            alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=msg
        )
        self.assertLess(
            alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=msg
        )
        self.assertEqual(len(alignment), 2, msg=msg)
        self.assertIs(alignment.sequences[0], alignment.target, msg=msg)
        self.assertIs(alignment.sequences[1], alignment.query, msg=msg)
        self.assertEqual(alignment.target.id, "chr22", msg=msg)
        if bedN >= 4:
            self.assertEqual(alignment.query.id, "mRNA1", msg=msg)
        else:
            self.assertIsNone(alignment.query.id, msg=msg)
        if bedN == 12:
            self.assertTrue(
                np.array_equal(
                    alignment.coordinates,
                    # fmt: off
                    np.array([[1000, 1567, 4512, 5000],
                              [   0,  567,  567, 1055]]),
                    # fmt: on
                ),
                msg=msg,
            )
        else:
            self.assertTrue(
                np.array_equal(
                    alignment.coordinates,
                    np.array([[1000, 5000], [0, 4000]]),
                ),
                msg=msg,
            )
        if bedN >= 7:
            self.assertEqual(alignment.thickStart, 1200, msg=msg)
        if bedN >= 8:
            self.assertEqual(alignment.thickEnd, 4900, msg=msg)
        if bedN >= 9:
            self.assertEqual(alignment.itemRgb, "255,0,0", msg=msg)
        alignment = next(alignments)
        if bedN >= 5:
            self.assertEqual(alignment.score, 900, msg=msg)
        self.assertEqual(alignment.shape, (2, 4000), msg=msg)
        self.assertLess(
            alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=msg
        )
        if bedN >= 6:
            self.assertGreater(
                alignment.coordinates[1, 0],
                alignment.coordinates[1, -1],
                msg=msg,
            )
        else:
            self.assertLess(
                alignment.coordinates[1, 0],
                alignment.coordinates[1, -1],
                msg=msg,
            )
        self.assertEqual(len(alignment), 2, msg=msg)
        self.assertIs(alignment.sequences[0], alignment.target, msg=msg)
        self.assertIs(alignment.sequences[1], alignment.query, msg=msg)
        self.assertEqual(alignment.target.id, "chr22", msg=msg)
        if bedN >= 4:
            self.assertEqual(alignment.query.id, "mRNA2", msg=msg)
        else:
            self.assertIsNone(alignment.query.id, msg=msg)
        if bedN == 12:
            self.assertTrue(
                np.array_equal(
                    alignment.coordinates,
                    # fmt: off
                    np.array([[2000, 2433, 5601, 6000],
                              [ 832,  399,  399,    0]])
                    # fmt: on
                ),
                msg=msg,
            )
        elif bedN >= 6:
            self.assertTrue(
                np.array_equal(
                    alignment.coordinates,
                    np.array([[2000, 6000], [4000, 0]]),
                ),
                msg=msg,
            )
        else:
            self.assertTrue(
                np.array_equal(
                    alignment.coordinates,
                    np.array([[2000, 6000], [0, 4000]]),
                ),
                msg=msg,
            )
        if bedN >= 7:
            self.assertEqual(alignment.thickStart, 2300, msg=msg)
        if bedN >= 8:
            self.assertEqual(alignment.thickEnd, 5960, msg=msg)
        if bedN >= 9:
            self.assertEqual(alignment.itemRgb, "0,255,0", msg=msg)
        with self.assertRaises(StopIteration) as cm:
            next(alignments)
            self.fail("More than two alignments reported")

    def test_reading(self):
        """Test parsing alignments in file formats BED3 through BED12."""
        for bedN in (3, 4, 5, 6, 7, 8, 9, 12):
            filename = "bed%d.bb" % bedN
            path = os.path.join("Blat", filename)
            alignments = Align.parse(path, "bigbed")
            msg = "bed%d" % bedN
            self.check_autosql(alignments.declaration, bedN, msg)
            self.check_alignments(alignments, bedN, msg)

    def test_writing(self):
        """Test Writing alignments in file formats BED3 through BED12."""
        for bedN in (3, 4, 5, 6, 7, 8, 9, 12):
            filename = "bed%d.bb" % bedN
            path = os.path.join("Blat", filename)
            alignments = Align.parse(path, "bigbed")
            with tempfile.TemporaryFile() as output:
                Align.write(alignments, output, "bigbed", bedN=bedN)
                output.flush()
                output.seek(0)
                alignments = Align.parse(output, "bigbed")
                msg = "bed%d" % bedN
                self.check_autosql(alignments.declaration, bedN, msg)
                self.check_alignments(alignments, bedN, msg)


class TestAlign_extended_bed(unittest.TestCase):
    # The bigBed files bigbed_extended.littleendian.bb and
    # bigbed_extended.bigendian.bb are BED9+2 files, with nine predefined BED
    # fields and 2 extra (custom) fields. It was created by running
    #
    # bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes bigbed_extended.bb
    #
    # where bedExample2.bed contains 10 lines selected from the example BED9+2
    # file bedExample2.bed downloaded from UCSC
    # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.bed)
    # and bedExample2.as the associated AutoSQL file, also downloaded from UCSC
    # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.as)
    # declaring the nine predefined BED fields and the two extra fields
    #
    # The bigBed file bigbed_extended.littleendian.bb was generated on a
    # little-endian machine; the bigBed file bigbed_extended.bigendian.bb was
    # generated on a big-endian machine.

    def test_reading(self):
        """Test parsing bigbed_extended.bb."""
        path = "Blat/bigbed_extended.littleendian.bb"
        alignments = Align.parse(path, "bigbed")
        self.assertEqual(alignments.byteorder, "<")
        self.check_alignments(alignments)
        path = "Blat/bigbed_extended.bigendian.bb"
        alignments = Align.parse(path, "bigbed")
        self.assertEqual(alignments.byteorder, ">")
        self.check_alignments(alignments)

    def check_alignments(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table hg18KGchr7
"UCSC Genes for chr7 with color plus GeneSymbol and SwissProtID"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position of feature on chromosome"
   uint    chromEnd;      "End position of feature on chromosome"
   string  name;          "Name of gene"
   uint    score;         "Score"
   char[1] strand;        "+ or - for strand"
   uint    thickStart;    "Coding region start"
   uint    thickEnd;      "Coding region end"
   uint    reserved;      "Green on + strand, Red on - strand"
   string  geneSymbol;    "Gene Symbol"
   string  spID;          "SWISS-PROT protein Accession number"
)
""",
        )
        self.assertEqual(len(alignments.targets), 1)
        self.assertEqual(alignments.targets[0].id, "chr7")
        self.assertEqual(len(alignments.targets[0]), 158821424)
        self.assertEqual(len(alignments), 10)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 60328)
        self.assertEqual(alignment.thickEnd, 60328)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 1241))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc010krx.1")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[60328, 61569], [1241, 0]]))
        )
        self.assertEqual(alignment.annotations["geneSymbol"], ".")
        self.assertEqual(alignment.annotations["spID"], "PDGFA")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (1241 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 1241:
        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, 1241)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 506606)
        self.assertEqual(alignment.thickEnd, 525164)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 22585))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003sir.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[503422, 526007], [22585, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA")
        self.assertEqual(alignment.annotations["spID"], "P04085")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (22585 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 22585:
        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, 22585)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 504726)
        self.assertEqual(alignment.thickEnd, 525164)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 22585))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003sis.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[503422, 526007], [22585, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA")
        self.assertEqual(alignment.annotations["spID"], "P04085-2")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (22585 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 22585:
        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, 22585)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 507195)
        self.assertEqual(alignment.thickEnd, 518820)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 12690))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003sit.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[506940, 519630], [12690, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA")
        self.assertEqual(alignment.annotations["spID"], "Q32M96")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (12690 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 12690:
        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, 12690)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 556592)
        self.assertEqual(alignment.thickEnd, 717668)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 162747))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003siu.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[555912, 718659], [162747, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B")
        self.assertEqual(alignment.annotations["spID"], "Q8N422")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (162747 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 162747:
        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, 162747)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 556592)
        self.assertEqual(alignment.thickEnd, 717668)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 163357))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003siv.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[555912, 719269], [163357, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B")
        self.assertEqual(alignment.annotations["spID"], "Q8N422")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (163357 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 163357:
        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, 163357)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 556592)
        self.assertEqual(alignment.thickEnd, 717668)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 177901))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003siw.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[555912, 733813], [177901, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B")
        self.assertEqual(alignment.annotations["spID"], "Q8N422")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (177901 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 177901:
        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, 177901)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 585418)
        self.assertEqual(alignment.thickEnd, 585418)
        self.assertEqual(alignment.itemRgb, "255,0,0")
        self.assertEqual(alignment.shape, (2, 22329))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003six.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[585418, 607747], [22329, 0]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], ".")
        self.assertEqual(alignment.annotations["spID"], "PRKAR1B")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (22329 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 22329:
        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, 22329)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 733217)
        self.assertEqual(alignment.thickEnd, 791816)
        self.assertEqual(alignment.itemRgb, "0,255,0")
        self.assertEqual(alignment.shape, (2, 59779))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc003siz.2")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[732863, 792642], [0, 59779]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], ".")
        self.assertEqual(alignment.annotations["spID"], "DKFZp762F1415")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (59779 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 59779:
        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, 59779)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 0)
        self.assertEqual(alignment.thickStart, 732883)
        self.assertEqual(alignment.thickEnd, 791816)
        self.assertEqual(alignment.itemRgb, "0,255,0")
        self.assertEqual(alignment.shape, (2, 59779))
        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, "chr7")
        self.assertEqual(alignment.query.id, "uc010krz.1")
        self.assertTrue(
            np.array_equal(
                alignment.coordinates, np.array([[732863, 792642], [0, 59779]])
            )
        )
        self.assertEqual(alignment.annotations["geneSymbol"], "HEATR2")
        self.assertEqual(alignment.annotations["spID"], "Q86Y56")
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (59779 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 59779:
        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, 59779)

    def test_writing(self):
        """Test writing bigbed_extended.bb."""
        byteorder = sys.byteorder  # "little" or "big"
        path = f"Blat/bigbed_extended.{byteorder}endian.bb"
        with open(path, "rb") as stream:
            correct = stream.read()
        alignments = Align.parse(path, "bigbed")
        with open("Blat/bedExample2.as") as stream:
            autosql_data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(autosql_data)
        with tempfile.TemporaryFile() as output:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=9,
                declaration=declaration,
                extraIndex=["name", "geneSymbol"],
            )
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments(alignments)
        alignments = Align.parse(path, "bigbed")
        targets = alignments.targets
        with tempfile.TemporaryFile() as output:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=9,
                declaration=declaration,
                targets=targets,
                extraIndex=["name", "geneSymbol"],
            )
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments(alignments)


class TestAlign_searching(unittest.TestCase):
    path = "Blat/bigbedtest.bb"

    # The bigBed file bigbedtest.bb contains the following data:
    # chr1     10     100     name1   1       +
    # chr1     29      39     name2   2       -
    # chr1    200     300     name3   3       +
    # chr2     50      50     name4   6       +
    # chr2    100     110     name5   4       +
    # chr2    200     210     name6   5       +
    # chr2    220     220     name7   6       +
    # chr3      0       0     name8   7       -

    def check_alignments(self, alignments):
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
)
""",
        )
        self.assertEqual(len(alignments.targets), 3)
        self.assertEqual(alignments.targets[0].id, "chr1")
        self.assertEqual(len(alignments.targets[0]), 1000)
        self.assertEqual(alignments.targets[1].id, "chr2")
        self.assertEqual(len(alignments.targets[1]), 2000)
        self.assertEqual(alignments.targets[2].id, "chr3")
        self.assertEqual(len(alignments.targets[2]), 1000)
        self.assertEqual(len(alignments), 8)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 1)
        self.assertEqual(alignment.shape, (2, 90))
        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, "name1")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[10, 100], [0, 90]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (90 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 90:
        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, 90)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 2)
        self.assertEqual(alignment.shape, (2, 10))
        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, "name2")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[29, 39], [10, 0]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (10 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 10:
        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, 10)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 3)
        self.assertEqual(alignment.shape, (2, 100))
        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, "name3")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[200, 300], [0, 100]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (100 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 100:
        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, 100)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 6)
        self.assertEqual(alignment.shape, (2, 0))
        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, "name4")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[50, 50], [0, 0]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (0 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 0:
        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, 0)
        self.assertEqual(counts.identities, 0)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 4)
        self.assertEqual(alignment.shape, (2, 10))
        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, "name5")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[100, 110], [0, 10]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (10 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 10:
        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, 10)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 5)
        self.assertEqual(alignment.shape, (2, 10))
        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, "name6")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[200, 210], [0, 10]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (10 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 10:
        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, 10)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 6)
        self.assertEqual(alignment.shape, (2, 0))
        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, "name7")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[220, 220], [0, 0]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (0 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 0:
        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, 0)
        self.assertEqual(counts.identities, 0)
        self.assertEqual(counts.mismatches, 0)
        alignment = next(alignments)
        self.assertEqual(alignment.score, 7)
        self.assertEqual(alignment.shape, (2, 0))
        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, "name8")
        self.assertTrue(
            np.array_equal(alignment.coordinates, np.array([[0, 0], [0, 0]]))
        )
        counts = alignment.counts()
        self.assertEqual(
            repr(counts),
            "<AlignmentCounts object (0 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
            % id(counts),
        )
        self.assertEqual(
            str(counts),
            """\
AlignmentCounts object with
    aligned = 0:
        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, 0)
        self.assertEqual(counts.identities, 0)
        self.assertEqual(counts.mismatches, 0)

    def test_reading(self):
        """Test reading bigbedtest.bb."""
        alignments = Align.parse(self.path, "bigbed")
        self.check_alignments(alignments)

    def test_writing(self):
        """Test writing bigbedtest.bb."""
        alignments = Align.parse(self.path, "bigbed")
        with tempfile.TemporaryFile() as output:
            Align.write(alignments, output, "bigbed", bedN=6)
            output.flush()
            output.seek(0)
            alignments = Align.parse(output, "bigbed")
            self.check_alignments(alignments)

    def test_search_chromosome(self):
        alignments = Align.parse(self.path, "bigbed")
        self.assertEqual(
            str(alignments.declaration),
            """\
table bed
"Browser Extensible Data"
(
   string  chrom;         "Reference sequence chromosome or scaffold"
   uint    chromStart;    "Start position in chromosome"
   uint    chromEnd;      "End position in chromosome"
   string  name;          "Name of item."
   uint    score;         "Score (0-1000)"
   char[1] strand;        "+ or - for strand"
)
""",
        )
        selected_alignments = alignments.search("chr2")
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name4", "name5", "name6", "name7"])

    def test_search_region(self):
        alignments = Align.parse(self.path, "bigbed")
        selected_alignments = alignments.search("chr2", 105, 1000)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name5", "name6", "name7"])
        selected_alignments = alignments.search("chr2", 110, 1000)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name6", "name7"])
        selected_alignments = alignments.search("chr2", 40, 50)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name4"])
        selected_alignments = alignments.search("chr2", 50, 50)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name4"])
        selected_alignments = alignments.search("chr2", 50, 200)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name4", "name5"])
        selected_alignments = alignments.search("chr2", 200, 220)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name6", "name7"])
        selected_alignments = alignments.search("chr2", 220, 220)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name7"])

    def test_search_position(self):
        alignments = Align.parse(self.path, "bigbed")
        selected_alignments = alignments.search("chr1", 250)
        names = [alignment.query.id for alignment in selected_alignments]
        self.assertEqual(names, ["name3"])

    def test_three_iterators(self):
        """Create three iterators and use them concurrently."""
        alignments1 = Align.parse(self.path, "bigbed")
        alignments2 = alignments1.search("chr2")
        alignments3 = alignments1.search("chr2", 110, 1000)
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name1")
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name2")
        alignment2 = next(alignments2)
        self.assertEqual(alignment2.query.id, "name4")
        alignment2 = next(alignments2)
        self.assertEqual(alignment2.query.id, "name5")
        alignment2 = next(alignments2)
        self.assertEqual(alignment2.query.id, "name6")
        alignment3 = next(alignments3)
        self.assertEqual(alignment3.query.id, "name6")
        alignment3 = next(alignments3)
        self.assertEqual(alignment3.query.id, "name7")
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name3")
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name4")
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name5")
        alignment2 = next(alignments2)
        self.assertEqual(alignment2.query.id, "name7")
        self.assertRaises(StopIteration, next, alignments2)
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name6")
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name7")
        self.assertRaises(StopIteration, next, alignments3)
        alignment1 = next(alignments1)
        self.assertEqual(alignment1.query.id, "name8")
        self.assertRaises(StopIteration, next, alignments1)


class BinaryTestBaseClass(unittest.TestCase):
    def assertBinaryEqual(self, file1, file2):
        blocksize = 1024
        n = 0
        while True:
            data1 = file1.read(blocksize)
            data2 = file2.read(blocksize)
            if data1 == b"" and data2 == b"":
                return
            n1 = len(data1)
            if data1 == data2:
                n += n1
                continue
            n2 = len(data2)
            if n1 < n2:
                return self.fail(f"unequal file sizes: {n1} bytes vs >= {n2} bytes")
            if n1 > n2:
                return self.fail(f"unequal file sizes: >= {n1} bytes vs {n2} bytes")
            for i, (c1, c2) in enumerate(zip(data1, data2)):
                if c1 != c2:
                    return self.fail(f"bytes at position {n + i} differ: {c1} vs {c2}")


@unittest.skipUnless(big is True, "big file; use --big to run")
class TestAlign_big(BinaryTestBaseClass):
    # BED files were downloaded from the UCSC table browser:
    #
    # ucsc.bed contains the GENCODE V43 Basic gene annotations for human genome
    # assembly hg38.
    #
    # anoGam3.bed contains the AUGUSTUS gene annotations for genome assembly
    # anoGam3 of Anopheles gambiae (African malaria mosquito).
    #
    # ailMel1.bed contains the NCBI RefSeq All gene annotations for genome
    # assembly ailMel1 of Ailuropoda melanoleuca (giant panda).
    #
    # bisBis1.bed contains the AUGUSTUS gene annotations for genome assembly
    # bisBis1 of Bison bison bison (American bison).
    #
    # bigBed files were generated using bedToBigBed v. 2.9 found in
    # jksrc.v445.zip of the 'kent' source tree provided by UCSC
    # (http://hgdownload.cse.ucsc.edu/admin/).

    def test_a_compressed(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # bedToBigBed -as=Blat/bed12.as ucsc.clean.bed Align/hg38.chrom.sizes ucsc.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_b_uncompressed(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # bedToBigBed -as=Blat/bed12.as -unc ucsc.clean.bed Align/hg38.chrom.sizes ucsc.unc.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.unc.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                compress=False,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_c_bed3(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-3 ucsc.clean.bed > ucsc.bed3.bed
        # bedToBigBed -as=Blat/bed3.as -type=bed3 ucsc.bed3.bed Align/hg38.chrom.sizes ucsc.bed3.bb
        with open("Blat/bed3.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed3.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=3,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_d_bed4(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-4 ucsc.clean.bed > ucsc.bed4.bed
        # bedToBigBed -as=Blat/bed4.as -type=bed4 ucsc.bed4.bed Align/hg38.chrom.sizes ucsc.bed4.bb
        with open("Blat/bed4.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed4.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=4,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_e_bed5(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-5 ucsc.clean.bed > ucsc.bed5.bed
        # bedToBigBed -as=Blat/bed5.as -type=bed5 ucsc.bed5.bed Align/hg38.chrom.sizes ucsc.bed5.bb
        with open("Blat/bed5.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed5.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=5,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_f_bed6(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-6 ucsc.clean.bed > ucsc.bed6.bed
        # bedToBigBed -as=Blat/bed6.as -type=bed6 ucsc.bed6.bed Align/hg38.chrom.sizes ucsc.bed6.bb
        with open("Blat/bed6.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed6.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=6,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_g_bed7(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-7 ucsc.clean.bed > ucsc.bed7.bed
        # bedToBigBed -as=Blat/bed7.as -type=bed7 ucsc.bed7.bed Align/hg38.chrom.sizes ucsc.bed7.bb
        with open("Blat/bed7.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed7.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=7,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_h_bed8(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-8 ucsc.clean.bed > ucsc.bed8.bed
        # bedToBigBed -as=Blat/bed8.as -type=bed8 ucsc.bed8.bed Align/hg38.chrom.sizes ucsc.bed8.bb
        with open("Blat/bed8.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed8.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=8,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_i_bed9(self):
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed
        # cut -f 1-9 ucsc.clean.bed > ucsc.bed9.bed
        # bedToBigBed -as=Blat/bed9.as -type=bed9 ucsc.bed9.bed Align/hg38.chrom.sizes ucsc.bed9.bb
        with open("Blat/bed9.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        bigBedFileName = "ucsc.bed9.bb"
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                bedN=9,
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_j_extraindex(self):
        # If the names in the BED file are not unique, the binary contents of
        # the generated bigBed file will depend on the exact implementation of
        # the quicksort algorithm in the Standard Library of C (used by
        # bedToBigBed) and the quicksort algorithm in numpy (used by Biopython).
        # To prevent spurious errors when comparing bigBed files created by
        # bedToBigBed and by Biopython, we first remove lines with duplicated
        # names from the BED file.
        # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed
        # sort -u -k4,4 ucsc.clean.bed | sort -k1,1 -k2,2n > ucsc.unique.bed
        # bedToBigBed -as=Blat/bed12.as -extraIndex=name ucsc.unique.bed Align/hg38.chrom.sizes ucsc.indexed.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ucsc.indexed.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                extraIndex=["name"],
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_k_anogam(self):
        # sort -k1,1 -k2,2n Blat/anoGam3.bed -o anoGam3.bed
        # bedToBigBed -as=Blat/bed12.as anoGam3.bed Blat/anoGam3.chrom.sizes anoGam3.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "anoGam3.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_l_ailmel(self):
        # sort -k1,1 -k2,2n Blat/ailMel1.bed -o ailMel1.bed
        # bedToBigBed -as=Blat/bed12.as ailMel1.bed Blat/ailMel1.chrom.sizes ailMel1.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "ailMel1.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)

    def test_m_bisbis(self):
        # sort -k1,1 -k2,2n bisBis1.bed -o bisBis1.bed
        # bedToBigBed -as=Blat/bed12.as bisBis1.bed Blat/bisBis1.chrom.sizes bisBis1.bb
        with open("Blat/bed12.as") as stream:
            data = stream.read()
        declaration = bigbed.AutoSQLTable.from_string(data)
        bigBedFileName = "bisBis1.bb"
        alignments = Align.parse(bigBedFileName, "bigbed")
        with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream:
            Align.write(
                alignments,
                output,
                "bigbed",
                declaration=declaration,
                compress=True,
            )
            output.flush()
            output.seek(0)
            self.assertBinaryEqual(output, stream)


class TestDeclarations(unittest.TestCase):
    def test_declarations(self):
        for length in (3, 4, 5, 6, 7, 8, 9, 12):
            filename = "bed%d.as" % length
            path = os.path.join("Blat", filename)
            with open(path) as stream:
                data = stream.read()
            declaration = bigbed.AutoSQLTable.from_string(data)
            self.assertEqual(declaration.name, "bed", msg=filename)
            self.assertEqual(
                declaration.comment, "Browser Extensible Data", msg=filename
            )
            self.assertEqual(len(declaration), length, msg=filename)
            field = declaration[0]
            self.assertEqual(field.as_type, "string", msg=filename)
            self.assertEqual(field.name, "chrom", msg=filename)
            self.assertEqual(
                field.comment, "Reference sequence chromosome or scaffold", msg=filename
            )
            field = declaration[1]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "chromStart", msg=filename)
            self.assertEqual(
                field.comment, "Start position in chromosome", msg=filename
            )
            field = declaration[2]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "chromEnd", msg=filename)
            self.assertEqual(field.comment, "End position in chromosome", msg=filename)
            if length == 3:
                return
            field = declaration[3]
            self.assertEqual(field.as_type, "string", msg=filename)
            self.assertEqual(field.name, "name", msg=filename)
            self.assertEqual(field.comment, "Name of item.", msg=filename)
            if length == 4:
                return
            field = declaration[4]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "score", msg=filename)
            self.assertEqual(field.comment, "Score (0-1000)", msg=filename)
            if length == 5:
                return
            field = declaration[5]
            self.assertEqual(field.as_type, "char[1]", msg=filename)
            self.assertEqual(field.name, "strand", msg=filename)
            self.assertEqual(field.comment, "+ or - for strand", msg=filename)
            if length == 6:
                return
            field = declaration[6]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "thickStart", msg=filename)
            self.assertEqual(
                field.comment,
                "Start of where display should be thick (start codon)",
                msg=filename,
            )
            if length == 7:
                return
            field = declaration[7]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "thickEnd", msg=filename)
            self.assertEqual(
                field.comment,
                "End of where display should be thick (stop codon)",
                msg=filename,
            )
            if length == 8:
                return
            field = declaration[8]
            self.assertEqual(field.as_type, "uint", msg=filename)
            self.assertEqual(field.name, "reserved", msg=filename)
            self.assertEqual(
                field.comment, "Used as itemRgb as of 2004-11-22", msg=filename
            )
            if length == 9:
                return
            field = declaration[9]
            self.assertEqual(field.as_type, "int", msg=filename)
            self.assertEqual(field.name, "blockCount", msg=filename)
            self.assertEqual(field.comment, "Number of blocks", msg=filename)
            field = declaration[10]
            self.assertEqual(field.as_type, "int[blockCount]", msg=filename)
            self.assertEqual(field.name, "blockSizes", msg=filename)
            self.assertEqual(
                field.comment, "Comma separated list of block sizes", msg=filename
            )
            field = declaration[11]
            self.assertEqual(field.as_type, "int[blockCount]", msg=filename)
            self.assertEqual(field.name, "chromStarts", msg=filename)
            self.assertEqual(
                field.comment, "Start positions relative to chromStart", msg=filename
            )


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