This release ushers in a new era in the development of poseidon-hs: We merged the poseidon-analysis-hs library into poseidon-hs, which was previously developed in a separate repository [here](https://github.com/poseidon-framework/poseidon-analysis-hs). We did this to keep xerxes, a software tool for Poseidon data analysis, fully in sync with trident. In the past xerxes often lagged behind and didn't use the most recent innovations and fixes available in poseidon-hs. We hope merging the repositories will make maintenance easier. So both software tools trident and xerxes will be versioned together from now on, starting with this release v2.0.0.0. The large jump in the version number reflects the conceptual change in development strategy, and the pretty significant restructering that was necessary in the Haskell library code to house poseidon-analysis-hs in poseidon-hs. From a user perspective there were only minor changes in functionality: #### trident Since v1.7.0.0 we only fixed two minor bugs in `genoconvert` and `forge` regarding the handling of the new `POSEIDON.yml` fields `referenceGenomeAssembly` and `referenceGenomeAssemblyURL`. These were not properly forwarded/preserved in the respective operations. The `genoconvert` bug was reported in this [issue](https://github.com/poseidon-framework/poseidon-hs/issues/371). #### xerxes The last official xerxes release was v1.0.1.2. See `xerxes_legacy_changelog/` for a documentation of previous development. Internal development had reached v1.0.2.0, which added VCF writing support for `admixpops`. #### Building process Note that we had to remove the UPX compression we had applied in the past to some of the static executables build for trident and xerxes upon release. That means the v2.0.0.0 executables will most likely be larger.

This release finally brings two long-anticipated features: VCF writing support and an html API for `serve`. It also includes some minor bugfixes. #### Writing support for VCF files v1.5.7.0 added experimental reading support for .vcf files. In this release trident finally learns to also write them as an output of `forge` and `genoconvert`. This new output option is available with `--outFormat VCF`. VCF is a rich format (as specified [here](https://samtools.github.io/hts-specs/VCFv4.2.pdf)) and trident currently uses only the features relevant for the genotype data typically handled by Poseidon. In particular, as trident must be able to convert from Plink and Eigenstrat, many fields that are typically expected in VCF files (such as read- and allelic depths or genotype likelihoods) are not written. On the other hand VCF files written by trident contain the extra headers `##group_names=Group1,Group2,...` and `##genetic_sex=F,F,M,U,...` to encode information typically not stored in VCF. This is to ensure compatibility with the PLINK and EIGENSTRAT data formats. trident has modified behavior for consistency checks between Ind- and Geno-file for VCFs, since VCF files do not _have_ to have these custom header fields defined above. Please note that the VCF format support is still not specified in the Poseidon schema version this trident version supports (v2.7.1), so the feature continues to be experimental. #### HMTL API for the web server implementation trident includes a web server to host Poseidon packages and relevant meta-information. It can be started with the subcommand `serve`. The central Poseidon server at https://server.poseidon-adna.org is nothing but a public instance of `serve` with access to the public package archives. Previously this web server provided only context data through a JSON API and allowed downloading packages as .zip archives (these interfaces are used by `list --remote` and `fetch`). This release now adds HTML output, so a human-readable website, to the server's API. The central, public version is available [here](https://server.poseidon-adna.org/explorer), but by running `serve` locally one can just as well host such a website for a private package archive. `serve` can still be started with `trident serve -d <name_of_archive>=<path/to/archive>`, but now a new `--archiveConfigFile` argument allows to read more complex configuration in YML format. #### More info from the POSEIDON.yml file in the `list` output Added a new option `--fullOutput` for `list --packages` to extend the output with additional information from the underlying packages' POSEIDON.yml files (file names, contributors, etc.). #### Fixed two bugs in `rectify` Fixed a small bug that prevented calculation of checksums for genotype data in `rectify`, and another one that prevented trident from reading packages with a wrong individual file (.ind/.fam) checksum even in `rectify`, where this should be possible.

This is a bigger release with various new features and improvements. It is technically breaking, because a minor, redundant argument of `genoconvert` was removed. #### Writing support for gzipped genotype data After reading support for zipped data was already added in V 1.5.7.0, this release now introduces the complementary writing feature for EIGENSTRAT and PLINK files in `genoconvert` and `forge`. Both commands get a new option `-z` which creates gzipped output. ``` -z,--zip Should the resulting genotype- and snp-files be gzipped? ``` Note that this feature includes a smart way of handling already available files to not overwrite them, but still consider them when updating a package's POSEIDON.yml file. `-z` is also usable with unpackaged genotype data (`-p`, `--onlyGeno`). Future versions of the Poseidon package schema will formally specify this feature. #### Bibliography information in `list` and the Web-API The `list` subcommand now supports a new view (next to `--packages`, `--groups` and `individuals`): `--bibliography` allows to get a tabular overview of publications in a package repository. ``` $ trident list -d 2010_RasmussenNature --bibliography ... .---------------------.--------------------------------------------------------------.-----------------------.------.---------------------------.---------------. | BibKey | Title | Author | Year | DOI | Nr of samples | :=====================:==============================================================:=======================:======:===========================:===============: | AADR | The Allen Ancient DNA Resource (AADR): A curated compendium… | Swapan Mallick et al. | 2023 | 10.1101/2023.04.06.535797 | 1 | | AADRv424 | The Allen Ancient DNA Resource (AADR): A curated compendium… | S Mallick and D Reich | 2023 | 10.7910/DVN/FFIDCW | 1 | | RasmussenNature2010 | Ancient human genome sequence of an extinct Palaeo-Eskimo | M Rasmussen et al. | 2010 | 10.1038/nature08835 | 1 | '---------------------'--------------------------------------------------------------'-----------------------'------'---------------------------'---------------' ``` Additional fields from the .bib file can be added to this table with `-b|--bibField ...` (just as `-j|--jannoColumn ...` for `--individuals`). `--fullBib` adds everything that is available (just as `--fullJanno`). As usual, tab-separated output can be requested with `--raw` for derived analyses on the command line. Correspondingly the Web-API supports a new endpoint `/bibliography` to serve bibliography information via HTTP in JSON format. The optional query argument `additionalJannoColumns=...` allows to request extra fields here. #### Remove empty .janno columns with `rectify` The `rectify` subcommand was upgraded with a first option to manipulated .janno files in one or multiple packages: `--jannoRemoveEmpty`. This allows to remove empty columns from .janno files, so columns that only feature empty strings or `n/a` values. ``` --jannoRemoveEmpty Reorder the .janno file and remove empty colums. Remember to pair this option with --checksumJanno to also update the checksum. ``` With this change came a rewrite of the way trident fills empty fields with `n/a` when writing .janno and .ssf files. This behaviour now also affects the output of `list`! #### Removed redundant `--onlyGeno` from `genoconvert` We realized that `--onlyGeno` in `genoconvert` had the same effect as `-o` if a different output directory is chosen. We therefore decided to remove this argument and improve the documentation of `-o`: ``` -o,--outPackagePath DIR Path for the converted genotype files to be written to. If a path is provided, only the converted genotype files are written out, with no change of the original package. If no path is provided, genotype files will be converted in-place, including a change in the POSEIDON.yml file to yield an updated valid package (default: Nothing) ``` #### Bug fixes and technical changes We fixed two bugs that broke the long-form genotype data input option (with `--genoFile + --snpFile + ...`). They were accidentally added with the recent interface changes for V 1.5.7.0. This input interface should now be fully functional again. We finally switched to a new compiler version (GHC 9.6.6) and a new stackage resolver version (lts-22.43). This required some minor adjustments in the server code, but should not have any user-facing consequences.

This release further improves `.janno` parsing error messages and adds reading support for gzipped PLINK (`.bed` and `.bim`) and EIGENSTRAT (`.geno` and `.snp`) files. We also added (experimental) support for reading VCF files. #### Better .janno error messages Working with Poseidon packages generally involves reading and validation of `.janno` files. `trident` parses them carefully and reports structural issues that compromise their machine-readability. So far the error reports generally only included the line and type of an offending entry. This made it sometimes hard to determine which column exactly is broken. For this release we introduced individual data types for all specified `.janno` columns, which allows more precises error messages. To demonstrate this we modified an existing `.janno` file in the Poseidon community archive (`2012_MeyerScience`) and broke some of its columns. We added non-UTF8 encoded characters in the `Relation_Note` column of line 2, a trailing `;` in the `Coverage_on_Target_SNPs` column of line 3, and a leading `x` to the `Latitude` column of line 7. Here is how these issues were previously reported and how they are shown now: ```diff [Error] Can't read sample in 2012_MeyerScience/2012_MeyerScience2.csv in line 2: -parse error (Failed reading: conversion error: Cannot decode byte '\x80': Data.Text.Encoding: Invalid UTF-8 stream) +parse error (Failed reading: conversion error: Cannot decode byte '\x80': Data.Text.Encoding: Invalid UTF-8 stream in column Relation_Note) [Error] Can't read sample in 2012_MeyerScience/2012_MeyerScience2.csv in line 3: -parse error in one column (expected data type: Double, broken value: "32.12;", problematic characters: ";") +parse error (Failed reading: conversion error: Coverage_on_Target_SNPs can not be converted to Double, because of a trailing ";") [Error] Can't read sample in 2012_MeyerScience/2012_MeyerScience2.csv in line 7: -parse error (Failed reading: conversion error: expected Double, got "x18.93726" (Failed reading: takeWhile1)) +parse error (Failed reading: conversion error: Latitude can not be converted to Double because input does not start with a digit) ``` The error messages now include the relevant column name and are more concrete and easy to understand. #### Reading support for gzipped genotype data Although not yet part of the Poseidon 2.7.1 standard, Poseidon packages can now contain gzipped genotype files. Specifically, for EIGENSTRAT-formatted genotype data, the genotype matrix file (`.geno`) and the snp-list file (`.snp`) can now also be zipped. This strictly requires file endings with `.gz`, so `.geno.gz` and `.snp.gz`, respectively. Similarly, for PLINK-formatted genotype data, we now also accept `.bed.gz` and `.bim.gz`. Any such files with the `gz` file ending are assumed to be gzipped, and are decoded on the fly using stream-processing. Gzipped and unzipped files can also be mixed within the same package. For commands that support the `--genoOne` option (`init`, `forge` and `genoconvert`), note that we make some assumptions, which are summarised in the help text for the option: ``` -p,--genoOne FILE One of the input genotype data files. Expects .bed, .bed.gz, .bim, .bim.gz or .fam for PLINK, or .geno, .geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT. The other files must be in the same directory and must have the same base name. If a gzipped file is given, it is assumed that the file pairs (.geno.gz, .snp.gz) or (.bim.gz, .bed.gz) are both zipped, but not the .fam or .ind file. If a .ind or .fam file is given, it is assumed that none of the file triples is zipped. For VCF please see option --vcfFile ``` At this point, `genoconvert` and `forge` do _not_ support writing of gzipped files. This will be added in the future. #### VCF support for genotype data Although not yet part of the Poseidon 2.7.1 standard, Poseidon packages can now contain VCF (Variant Call Format) files as genotype data, optionally gzipped. In contrast to EIGENSTRAT and PLINK format, which require triples of files, the VCF format requires just one file with ending `.vcf` or `.vcf.gz`. VCF files contain sample names, but no information about genetic sex or group names. This information is usually provided in `.janno` files, so there is no loss of information in Poseidon packages. For `trident init`, which constructs a minimal `.janno` file from the genotypem file, we set the `Genetic_Sex` column to "U", and the `Group_Name` column to "unknown". The VCF file format is very flexible and can encode a large amount of information (see https://samtools.github.io/hts-specs/VCFv4.2.pdf). We do not consider our parsing of VCF files to be complete. The feature is for now experimental, since future users may encounter valid VCF files that cause parsing errors in edge cases. Do not hesitate to file an issue in such a case: https://github.com/poseidon-framework/poseidon-hs/issues. At this point, `genoconvert` and `forge` do _not_ support writing of VCF files. This will be added in the future.

This bigger release adds a number of useful features to `trident`, some of them long requested. The highlights are ordered output for `forge`, a way to preserve key information if `forge` is applied to a singular source package, a new Web-API option to return the content of all available `.janno` columns, and better error messages for common `trident` issues. #### Order `forge` output with `--ordered` The order of samples in a Poseidon package created with `trident forge` depends on the order in which the relevant source packages are discovered by `trident` (e.g. when it crawls for packages in the `-d` base directories) and then the sample order within these packages. This mechanism did not allow for any convenient way to manually set the output order. v1.5.4.0 adds a new option `--ordered`, which causes `trident` to output the resulting package with samples ordered according to the selection in `-f` or `--forgeFile`. This works through an alternative, slower sample selection algorithm that loops through the list of entities and checks for each entity which samples it adds or removes respectively from the final selection. For simple, positive selection, packages, groups and samples are added as expected. Negative selection removes samples from the list again. If an entity is selected twice via positive selection, then its first occurrence is considered for the ordering. #### Preserve the source package in `forge` with `--preservePyml` For the specific task of subsetting a singular, existing Poseidon package it can be useful to preserve some fields of the `POSEIDON.yml` file of the source package, as well as supplementary information in the `README.md` and the `CHANGELOG.md` file. These are typically discarded by `forge`, but can now be copied over to the output package with the new `--preservePyml` output mode. Naturally this only works with a single source package! `--preservePyml` specifically preserves the following `POSEIDON.yml` fields: - `description` - `contributor` - `packageVersion` - `lastModified` - `readmeFile` - `changelogFile` Note that this does not include the package `title`, which can be easily set to be identical to the source with `-n` or `-o` if it is desired. The `poseidonVersion` field is also not copied, because `trident` can only ever produce output packages with the latest Poseidon schema version. While implementing this we clearly separated the different `forge` output modes (`--onlyGeno`, `--minimal`, `--preservePyml` and the default) and made them mutually exclusive. We did so to avoid an increasingly complex set of interactions between them for the future. One particular application of `--preservePyml` is the reordering of samples in an existing Poseidon package `MyPac` with the new `--ordered` flag. We suggest the following workflow for this application: 1. Generate a `--forgeFile` with the desired order of the samples in `MyPac`. This can be done manually or with any suitable tool. Here is an example, where we employ `qjanno` to generate a `forge` selection so that the samples are ordered alphabetically by their `Poseidon_ID`: ```bash qjanno "SELECT '<'||Poseidon_ID||'>' FROM d(MyPac) ORDER BY Poseidon_ID" --raw --noOutHeader > myOrder.txt ``` 2. Use `trident forge` with `--ordered` and `--preservePyml` to create the package with the specified order: ```bash trident forge -d MyPac --forgeFile myOrder.txt -o MyPac2 --ordered --preservePyml ``` 3. Apply `trident rectify` to increment the package version number and document the reordering: ```bash trident rectify -d MyPac2 --packageVersion Minor --logText "reordered the samples alphabetically by Poseidon_ID" ``` `MyPac2` then acts as a stand-in replacement for `MyPac` that only differs in the order of samples (and maybe the order of variables/fields in the `POSEIDON.yml`, `.janno`, `.ssf` or `.bib` files). This workflow is not as convenient as in-place reordering would be -- but much safer. #### Request all `.janno` columns in `list` and the Web-API `trident list --individuals` allows to access per-sample information for Poseidon packages on the command line. With the `-j` option arbitrary additional columns from the `.janno` files can be appended to the output. Here, for example, the `Country` and the `Genetic_Sex` columns: ``` trident list -d 2010_RasmussenNature --individuals -j "Country" -j "Genetic_Sex" .------------.---------------------.----------------------.----------------.-----------.-----------.-------------. | Individual | Group | Package | PackageVersion | Is Latest | Country | Genetic_Sex | :============:=====================:======================:================:===========:===========:=============: | Inuk.SG | Greenland_Saqqaq.SG | 2010_RasmussenNature | 2.1.1 | True | Greenland | M | '------------'---------------------'----------------------'----------------'-----------'-----------'-------------' ``` v1.5.4.0 adds a `--fullJanno` flag to request all columns at once, without having to list them individually with many `-j` arguments. This convenience feature was also added to the Web-API, where it can be triggered with `?additionalJannoColumns=ALL` on the `/individuals` endpoint: https://server.poseidon-adna.org/individuals?additionalJannoColumns=ALL #### Better error messages In previous `trident` versions some common error messages were not well rendered on the command line. This concerned particularly errors when parsing command line input, the `POSEIDON.yml` file or genotype data. We applied multiple changes here to improve the cli output. The behaviour of the global `trident` option `--errLength` was also changed. It now only truncates genotype data-related messages, but does so as well if these are raised on the `[Warning]` log level. This should make the previously often illegible `trident` output upon broken genotype data more readable.

This very minor release only affects the static `trident` executables produced for every release. It introduces a distinction between pre-built `X64` and `ARM64` executables for macOS, where changes in the main processor architecture have recently rendered old builds invalid for new systems and vice versa. That means the executable `trident-macOS` will henceforward not longer exist, but instead the executables `trident-macOS-X64` and `trident-macOS-ARM64`. In the past we have not explicitly documented changes in the compilation pipeline - v1.5.0.0, for example, came with a major overhaul of the pipeline - but in this case a small version bump seems to be in order to announce the split in available artefacts.

This is a minor, but technically breaking release. It removes the example contributor *Josiah Carberry* from new packages created by `trident init` and `trident forge` Previously every package created by `init` or `forge` included an example entry in the `contributor` field of the `POSEIDON.yml` file: ```yml - name: Josiah Carberry email: carberry@brown.edu orcid: 0000-0002-1825-0097 ``` This served the purpose of reminding users to actually set a contributor and giving an example how to do so. To simplify scripting with Poseidon packages we now remove this slightly gimmicky default. To encourage setting the contributor field we instead introduce a reading/validation warning in case the `contributor` field is empty: ``` [Warning] Contributor missing in POSEIDON.yml file of package 2010_RasmussenNature-2.1.1 ```

This release adds an entirely new subcommand to merge two `.janno` files (`jannocoalecse`) and improves the error messages for broken `.janno` files. #### Merging `.janno` files with `jannocoalesce` The need for a tool to combine the information of two `.janno` files arose in the Poseidon ecosystem as we started to conceptualize the Poseidon [Minotaur Archive](https://github.com/poseidon-framework/minotaur-archive). This archive will be populated by paper-wise Poseidon packages for which the genotype data was regenerated through the Minotaur workflow (work in progress). We plan to reprocess various packages that are already in the Poseidon [Community Archive](https://github.com/poseidon-framework/community-archive) and for these packages we want to copy e.g. spatiotemporal information from the already available `.janno` files. `jannocoalesce` is the answer to this specific need, but can also be useful for various other applications. It generally works by reading a source `.janno` file with `-s|--sourceFile` (or all `.janno` files in a `-d|--baseDir`) and a target `.janno` file with `-t|--targetFile`. It then merges these files by a key column, which can be selected with `--sourceKey` and `--targetKey`. The default for both of these key columns is the `Poseidon_ID`. In case the entries in the key columns slightly and systematically differ, e.g. because the `Poseidon_ID`s in either have a special suffix (for example `_SG`), then the `--stripIdRegex` option allows to strip these with a regular expression to thus match the keys. `jannocoalesce` generally attempts to fill **all** empty cells in the target `.janno` file with information from the source. `--includeColumns` and `--excludeColumns` allow to select specific columns for which this should be done. In some cases it may be desirable to not just fill empty fields in the target, but overwrite the information already there with the `-f|--force` option. If the target file should be preserved, then the output can be directed to a new output `.janno` file with `-o|--outFile`. #### Better error messages for broken `.janno` files `.janno` file validation is a core feature of `trident`. With this release we try to improve the error messages for a two common situations: 1. Broken number fields. This can happen if some text or wrong character ends up in a number field. So far the error messages for this case have been pretty technical. Here for example if an integer field is filled with `430;`, where the integer number `430` is accidentally written with a trailing `;`: ``` parse error (Failed reading: conversion error: expected Int, got "430;" (incomplete field parse, leftover: [59])) ``` The new error message is more clear: ``` parse error in one column (expected data type: Int, broken value: "430;", problematic characters: ";") ``` 2. Inconsistent `Date_*`, `Contamination_*` and `Relation_*` columns. These sets of columns have to be cross-consistent, following a logic that is especially complex for the `Date_*` fields (see [here](https://www.poseidon-adna.org/#/janno_details?id=the-columns-in-detail)). So far any inconsistency was reported with this generic error message: ``` The Date_* columns are not consistent ``` Now we include far more precise messages, like e.g.: ``` Date_Type is not "C14", but either Date_C14_Uncal_BP or Date_C14_Uncal_BP_Err are not empty. ``` This should simplify tedious `.janno` file debugging in the future.