feat: bcftools fixploidy wrapper #5176
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| # This file may be used to create an environment using: | ||
| # $ conda create --name <env> --file <this file> | ||
| # platform: linux-64 | ||
| # created-by: conda 24.9.2 | ||
| @EXPLICIT | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda#26c46f90d0e727e95c6c9498a33a09f3 | ||
| https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 | ||
| https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-h8577fbf_0.conda#338201218b54cadff2e774ac27733990 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda#6d0363467e6ed84f11435eb309f2ff06 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.22-hb9d3cd8_0.conda#b422943d5d772b7cc858b36ad2a92db5 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda#5a68259fac2da8f2ee6f7bfe49c9eb8b | ||
| https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_16.conda#39183d4e0c05609fd65f130633194e37 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.1-h0c1763c_0.conda#2e1b84d273b01835256e53fd938de355 | ||
| https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda#eecce068c7e4eddeb169591baac20ac4 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec | ||
| https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d | ||
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| https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 | ||
| https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-default_hbd61a6d_104.conda#a6abd2796fc332536735f68ba23f7901 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda#be43915efc66345cccb3c310b6ed0374 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda#c160954f7418d7b6e87eaf05a8913fa9 | ||
| https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.17.0-h4e3cde8_1.conda#117499f93e892ea1e57fdca16c2e8351 | ||
| https://conda.anaconda.org/conda-forge/linux-64/python-3.14.2-h32b2ec7_100_cp314.conda#1cef1236a05c3a98f68c33ae9425f656 | ||
| https://conda.anaconda.org/bioconda/linux-64/htslib-1.23-h566b1c6_0.conda#307124911d36a3d976cd76f350085ead | ||
| https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda#6636a2b6f1a87572df2970d3ebc87cc0 | ||
| https://conda.anaconda.org/conda-forge/noarch/pip-25.3-pyh145f28c_0.conda#bf47878473e5ab9fdb4115735230e191 | ||
| https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.8.0-pyhdfd78af_0.conda#1650e521333852f45468d97b1b2fdcce | ||
| https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de | ||
| https://conda.anaconda.org/bioconda/linux-64/bcftools-1.23-h3a4d415_0.conda#51a78d8b2f5a3d373ce369803b5e76e3 |
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| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - nodefaults | ||
| dependencies: | ||
| - bcftools =1.23 | ||
| - snakemake-wrapper-utils =0.8.0 |
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| name: bcftools fixploidy | ||
| url: https://samtools.github.io/bcftools/bcftools.html | ||
| author: | ||
| - Thibault Dayris | ||
| description: | | ||
| Set correct ploidy on variants calls | ||
| input: | ||
| - Path to variants file (VCF/VCF.GZ/BCF) | ||
| output: | ||
| - Path to corrected variants file (VCF/BCF/VCF.GZ) | ||
| params: | ||
| - extra: Optional parameters besides IO and their formats. | ||
| notes: | | ||
| This wrapper requires additional threads for IO compression. |
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| rule test_bcftools_fixploidy: | ||
| input: | ||
| "a.bcf", | ||
| output: | ||
| "a.fixed.bcf", | ||
| threads: 3 | ||
| params: | ||
| extra="", | ||
| log: | ||
| "test_bcftools_fixploidy.log", | ||
| wrapper: | ||
| "master/bio/bcftools/fixploidy" |
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| ../../filter/test/a.bcf |
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| __author__ = "Thibault Dayris" | ||||||
| __copyright__ = "Copyright 2026, Thibault Dayris" | ||||||
| __email__ = "thibault.dayris@gustaveroussy.fr" | ||||||
| __license__ = "MIT" | ||||||
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| from snakemake.shell import shell | ||||||
| from snakemake_wrapper_utils.bcftools import get_bcftools_opts | ||||||
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| bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False) | ||||||
| extra = snakemake.params.get("extra", "") | ||||||
| log = snakemake.log_fmt_shell(stdout=True, stderr=True) | ||||||
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| shell("bcftools plugin fixploidy {bcftools_opts} {extra} {snakemake.input[0]} {log}") | ||||||
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🧩 Analysis chain
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🌐 Web query:
bcftools fixploidy plugin documentation argument parsing💡 Result:
The bcftools +fixploidy plugin uses standard C getopt_long for argument parsing in its init function. Plugin options (after the "--" separator) are parsed using a static struct option long_options[] defining: - {"default-ploidy",1,0,'d'} - {"force-ploidy",1,0,'f'} - {"ploidy",1,0,'p'} - {"samples",1,0,'s'} Short options: -d, -f, -p, -s. The getopt_long loop processes these: case 'd': default_ploidy = strtod(optarg,&tmp); case 'f': force_ploidy = strtod(optarg,&tmp); case 'p': ploidy_fname = strdup(optarg); case 's': sex_fname = strdup(optarg); It initializes ploidy with defaults for chrX PAR regions if no -p file given, reads samples/sex from -s file, maps samples to sex, and sets sex-to-ploidy mapping. To view full usage: bcftools +fixploidy -h Source code: https://github.com/samtools/bcftools/blob/develop/plugins/fixploidy.c
Citations:
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bcftools plugin command line syntax "--" separator💡 Result:
In BCFtools, the "--" separator is used in plugin command lines to distinguish between general/common options (shared across many bcftools commands, such as -o, -O, -r) that come before it, and plugin-specific options that come after it. The general syntax for running a plugin is: bcftools +plugin_name [general options] input.vcf -- [plugin options] Examples from official documentation: bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t AN,AC bcftools +split-vep file.vcf.gz -- -a BCSQ bcftools +tag2tag in.vcf -- --LXX-to-XX -s 3 Some plugins do not accept general options and their usage is bcftools +plugin_name [input] [plugin options], without the "--" separator. Always check the plugin's usage with bcftools +plugin_name -h. To use plugins, set BCFTOOLS_PLUGINS=/path/to/bcftools/plugins or use full path like bcftools +/path/to/plugin.so.
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bcftools +fixploidy usage example input file position argument order💡 Result:
The standard usage of bcftools +fixploidy follows the general bcftools plugin syntax: bcftools +fixploidy [general options] [input.vcf[.gz]] [-- [plugin options]]. Input file position: The VCF/BCF input file is provided as a positional argument after general options (like -O u for uncompressed BCF output) and before the -- separator. If omitted, it reads from standard input (stdin). Examples from source code and usage: - bcftools +fixploidy in.vcf -- -s samples.txt Here, "in.vcf" is the input file. - bcftools +fixploidy haploid.vcf -- -f 2 > diploid.vcf Here, "haploid.vcf" is the input file, -f 2 forces diploid ploidy for all sites. General syntax template: bcftools +fixploidy -Ou -o output.bcf input.vcf -- -s samples.txt -p ploidy.txt Plugin options (after --): - -d, --default-ploidy [default: 2] - -f, --force-ploidy Ignore -p, set same ploidy everywhere - -p, --ploidy CHROM FROM TO SEX PLOIDY - -s, --sex NAME SEX (M/F) - -t, --tags [GT] Ploidy file format example: X 1 60000 M 1 X 2699521 154931043 M 1 Y 1 59373566 M 1 Y 1 59373566 F 0 Sex file example: sampleName1 M
Citations:
Move input file before
{extra}to follow bcftools plugin argument syntax.The bcftools fixploidy plugin requires input files to be positioned before the
--separator and plugin-specific options. If{extra}contains plugin options (e.g.,-- -s samples.txt), the current order places the input file after these options, causing incorrect parsing.Suggested fix
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@tdayris is this relevant?
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