2016-05-22 21:08:46 +00:00
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#
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# spec file for package bcftools
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#
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2025-04-02 13:44:43 +00:00
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# Copyright (c) 2025 SUSE LLC
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2016-05-22 21:08:46 +00:00
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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2021-05-16 16:34:09 +00:00
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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2016-05-22 21:08:46 +00:00
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#
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Name: bcftools
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2025-04-02 13:44:43 +00:00
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Version: 1.21
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2016-05-22 21:08:46 +00:00
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Release: 0
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Summary: Tools for manipulating variant calls in the Variant Call Format (VCF)
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License: MIT
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Group: Productivity/Scientific/Other
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2018-07-13 09:05:18 +00:00
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URL: http://www.htslib.org/
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Accepting request 770397 from home:TheBlackCat:branches:devel:languages:python:numeric
- Update to 1.10.2
* This release fixes crashes reported on files including integer
INFO tags with values outside the range officially supported
by VCF. It also fixes a bug where invalid BCF files would be
created if such values were present.
- Update to 1.10.0
+ Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors.
+ The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to bcftools isec and other commands.
+ Additions to filtering and formatting expressions
* support for the spanning deletion alternate allele (ALT=*)
* new ILEN filtering expression to be able to filter by indel length
* new MEAN, MEDIAN, MODE, STDEV, phred filtering functions
* new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files)
+ New plugins
* +gvcfz: compress gVCF file by resizing gVCF blocks according to specified criteria
* +indel-stats: collect various indel-specific statistics
* +parental-origin: determine parental origin of a CNV region
* +remove-overlaps: remove overlapping variants.
* +split-vep: query structured annotations such INFO/CSQ created by bcftools/csq or VEP
* +trio-dnm: screen variants for possible de-novo mutations in trios
+ annotate
* new -l, --merge-logic option for combining multiple overlapping regions
+ call
* new bcftools call -G, --group-samples option which allows grouping samples into populations and applying the HWE assumption within but not across the groups.
+ csq
* significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode.
* fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences
* do not print protein sequence of start_lost events
* support for "start_retained" consequence
* support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence
* new -b, --brief-predictions option to output abbreviated protein predictions.
+ concat
* the --naive command now checks header compatibility when concatenating multiple files.
+ consensus
* add a new -H, --haplotype 1pIu/2pIu feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes
* new -p, --prefix option to add a prefix to sequence names on output
+ +contrast
* added support for Fisher's test probability and other annotations
+ +fill-from-fasta
* new -N, --replace-non-ACGTN option
+ +dosage
* fix some serious bugs in dosage calculation
+ +fill-tags
* extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP.
+ merge
* add support for merging FORMAT strings
* bug fixed in gVCF merging
+ mpileup
* a new optional SCR annotation for the number of soft-clipped reads
+ reheader
* new -f, --fai option for updating contig lines in the VCF header
+ +trio-stats
* extend output to include DNM homs and recurrent DNMs
+ VariantKey support
OBS-URL: https://build.opensuse.org/request/show/770397
OBS-URL: https://build.opensuse.org/package/show/science/bcftools?expand=0&rev=7
2020-02-05 21:28:46 +00:00
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# The “Source code” downloads links generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files
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Source: https://github.com/samtools/bcftools/releases/download/%{version}/bcftools-%{version}.tar.bz2
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2020-02-12 17:40:04 +00:00
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# PATCH-FIX-OPENSUSE use_python3.patch -- Use python3 executable instead of python2
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Patch0: use_python3.patch
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2021-05-16 16:34:09 +00:00
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BuildRequires: automake
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2016-05-22 21:08:46 +00:00
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BuildRequires: gsl-devel
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2017-07-13 23:07:50 +00:00
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BuildRequires: libbz2-devel
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2022-09-09 14:20:13 +00:00
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BuildRequires: libhts-devel >= %{version}
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2017-07-13 23:07:50 +00:00
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BuildRequires: lzma-devel
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BuildRequires: zlib-devel
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2018-07-13 09:05:18 +00:00
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Requires: bgzip
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Requires: htsfile
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2025-04-02 13:44:43 +00:00
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Requires: perl-base
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2020-02-25 11:46:49 +00:00
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Requires: python3-base
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Requires: python3-matplotlib
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2018-07-13 09:05:18 +00:00
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Requires: tabix
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2016-05-22 21:08:46 +00:00
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%description
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Package for the new BCFtools: a set of utilities that manipulate variant calls in the Variant Call Format (VCF)
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and its binary counterpart BCF. It contains all the "vcf..." commands which previously lived in the HTSlib
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repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory
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of samtools. BCFtools are meant as a faster replacement for most of the perl VCFtools commands.
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%prep
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%autosetup -p1
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%build
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autoreconf -fi
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%configure --with-htslib=system
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%make_build USE_GSL=1
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%install
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%make_install prefix=%{_prefix} libexecdir=%{_libdir} libdir=%{_libdir}
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2018-07-13 09:05:18 +00:00
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# CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE
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sed -i "s:/usr/bin/env perl:%{_bindir}/perl:" %{buildroot}/%{_bindir}/*.pl %{buildroot}/%{_bindir}/plot-vcfstats
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sed -i -E "s:/usr/bin/env python3?:%{_bindir}/python3:" %{buildroot}/%{_bindir}/*.py
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%files
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2018-07-13 09:05:18 +00:00
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%license LICENSE
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%doc AUTHORS README NEWS
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%{_bindir}/bcftools
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%{_bindir}/*.py
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%{_bindir}/*.pl
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%{_bindir}/plot-vcfstats
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%{_libdir}/bcftools/
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%{_mandir}/man1/*
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%changelog
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