Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package bcftools for openSUSE:Factory checked in at 2022-05-04 15:10:44 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/bcftools (Old) and /work/SRC/openSUSE:Factory/.bcftools.new.1538 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "bcftools" Wed May 4 15:10:44 2022 rev:3 rq:974425 version:1.15.1 Changes: -------- --- /work/SRC/openSUSE:Factory/bcftools/bcftools.changes 2021-06-02 22:12:57.336046968 +0200 +++ /work/SRC/openSUSE:Factory/.bcftools.new.1538/bcftools.changes 2022-05-04 15:11:03.984165811 +0200 @@ -1,0 +2,176 @@ +Thu Apr 21 15:34:00 UTC 2022 - Ferdinand Thiessen <[email protected]> + +- Update to version 1.15.1 + * bcftools annotate: New -H, --header-line convenience option to + pass a header line on command line + * bcftools csq: A list of consequence types supported by bcftools + csq has been added to the manual page. + * bcftools +fill-tags: + * Extend generalized functions so that FORMAT tags can be filled + as well + * Allow multiple custom functions in a single run. + * bcftools norm: + * Fix an assertion failure triggered when a faulty VCF file with + a '-' character in the REF allele was used with bcftools + norm --atomize. + * Fix the loss of phasing in half-missing genotypes in variant + atomization + * bcftools roh: Fix a bug that could result in an endless loop or + incorrect AF estimate when missing genotypes are present and + the --estimate-AF - option was used + * bcftools +split-vep: VEP fields with characters disallowed in + VCF tag names by the specification couldn't be queried. +- Update to version 1.15 + * New bcftools head subcommand for conveniently displaying the + headers of a VCF or BCF file. + * The -T, --targets-file option had the following bug originating + in HTSlib code + * bcftools annotate: + * In addition to --rename-annots, which requires a file with + name mappings, it is now possible to do the same on the + command line -c NEW_TAG:=OLD_TAG + * Add new option --min-overlap which allows to specify the + minimum required overlap of intersecting regions + * Allow to transfer ALT from VCF with or without replacement + * bcftools convert: + * Revamp of --gensample, --hapsample and --haplegendsample + family of options + * New --3N6 option to output/input the new version of the .gen + file format + * Deprecate the --chrom option in favor of --3N6. + * The CHROM:POS_REF_ALT IDs which are used to detect strand + swaps are required and must appear either in the "SNP ID" + column or the "rsID" column. + * bcftools csq: Allow GFF files with phase column unset + * bcftools filter: New --mask, --mask-file and --mask-overlap + options to soft filter variants in regions + * bcftools +fixref + * The -m id option now works also for non-dbSNP ids + * New -m flip-all mode for flipping all sites + * bcftools isec: Prevent segfault on sites filtered with -i/-e + in all files + * bcftools mpileup: More flexible read filtering using the options + * bcftools query: Make the --samples and --samples-file options + work also in the --list-samples mode. + * bcftools +setGT: Fix a bug in -t q -e EXPR logic applied on + FORMAT fields, sites with all samples failing the expression + EXPR were incorrectly skipped. + * bcftools sort: make use of the TMPDIR environment variable + when defined + * bcftools +trio-dnm2: The --use-NAIVE mode now also adds the + de novo allele in FORMAT/VA +- Update to version 1.14 + * New --regions-overlap and --targets-overlap options which + address a long-standing design problem with subsetting VCF + files by region. + * The --output-type option can be used to override the default + compression level + * bcftools annotate: + * when --set-id and --remove are combined, --set-id cannot use + tags deleted by --remove. + * while non-symbolic variation are uniquely identified by + POS,REF,ALT, symbolic alleles starting at the same position + were indistinguishable. + * add a new . modifier to control whether missing values should + be carried over from a tab-delimited file or not. + * bcftools +check-ploidy: by default missing genotypes are not + used when determining ploidy. + * bcftools concat: new --ligate-force and --ligate-warn options + for finer control of -l, --ligate behavior in imperfect overlaps. + * bcftools consensus: Apply mask even when the VCF has no notion + about the chromosome. + * bcftools +contrast: support for chunking within map/reduce + framework allowing to collect NASSOC counts even for empty + case/control sample sets + * bcftools csq: + * bug fix, compound indels were not recognised in some cases + * compound variants were incorrectly marked as 'inframe' even when + stop codon would occur before the frame was restored + * bug fix, FORMAT/BCSQ bitmasks could have been assigned incorrectly + to some samples at multiallelic sites, a superset of the correct + consequences would have been set + * bug fix, the upstream stop could be falsely assigned to all samples + in a multi-sample VCF even if the stop was relevant for a single + sample only + * further improve the detection of mismatching chromosome naming + (e.g. "chrX" vs "X") in the GFF, VCF and fasta files + * bcftools merge: keep (sum) INFO/AN,AC values when merging VCFs + with no samples + * bcftools mpileup: new --indel-size option which allows to increase + the maximum considered indel size considered, large deletions in + long read data are otherwise lost. + * bcftools norm: + * atomization now supports Number=A,R string annotations + * assign as many alternate alleles to genotypes at multiallelic + sites in the-m + mode, disregarding the phase. + * bcftools sort: increase accuracy of the --max-mem option limit, + previously the limit could be exceeded by more than 20% + * bcftools +trio-dnm: new --with-pAD option to allow processing of + VCFs without FORMAT/QS. + * bcftools view: the functionality of the option --compression-level + lost in 1.12 has been restored +- Update to version 1.13 + * bcftools annotate: + * Fix rare a bug when INFO/END is present, all INFO fields are + removed with bcftools annotate -x INFO and BCF output is produced. + * Support for matching annotation line by ID, in addition to + CHROM,POS,REF, and ALT + * bcftools csq: + * When GFF and VCF/fasta use a different chromosome naming convention + no consequences would be added. + * Parametrize brief-predictions parameter to allow explicit number + of amino acids to be printed. + * bcftools +fill-tags: + * Generalization and better support for custom functions that allow + adding new INFO tags based on arbitrary -i, --include type of expressions. + * When FORMAT/GT is not present, the INFO/AF tag will be newly + calculated from INFO/AC and INFO/AN. + * bcftools gtcheck: + * Switch between FORMAT/GT or FORMAT/PL when one is (implicitly) + requested but only the other is available + * Improve diagnostics, printing warnings when a line cannot be + matched and the number of lines skipped for various reasons + * bcftools index: The program now accepts both data file name and + the index file name. + * bcftools isec: Always generate sites.txt with isec -p + * bcftools +mendelian: Consider only complete trios, + do not crash on sample name typos + * bcftools mpileup: + * New --seed option for reproducibility of subsampling code in HTSlib + * The SCR annotation which shows the number of soft-clipped reads + now correctly pools reads together regardless of the variant type. + * Major revamp of BAQ. + * Modified scale of Mann-Whitney U tests. + Newly INFO/*Z annotations will be printed + * bcftools norm: + * Fix Type=Flag output in norm --atomize + * Atomization must not discard ALT=. records + * Atomization of AD and QS tags now correctly updates occurrences + of duplicate alleles within different haplotypes + * Fix a bug in atomization of Number=A,R tags + * bcftools reheader: Add -T, --temp-prefix option + * bcftools +setGT: A wider range of genotypes can be set by the + plugin by allowing specifying custom genotypes. + * bcftools +split-vep: + * New -u, --allow-undef-tags option + * Better handling of ambiguous keys such as INFO/AF and CSQ/AD. + * Some consequence field names may not constitute a valid tag name, + such as "pos(1-based)". + * bcftools +tag2tag: New --QR-QA-to-QS option to convert annotations + generated by Freebayes to QS used by BCFtools + * bcftools +trio-dnm: + * Add support for sites with more than four alleles. + * New --use-NAIVE option for a naive DNM calling based solely on + FORMAT/GT and expected Mendelian inheritance. + * Fix behaviour to match the documentation, the --dnm-tag DNG option + now correctly outputs log scaled values by default, not phred scaled. + * Fix bug in VAF calculation, homozygous de novo variants were + incorrectly reported as having VAF=50% + * Fix arithmetic underflow which could lead to imprecise scores + and improve sensitivity in high coverage regions + * Allow combining --pn and --pns to set the noise thresholds independently +- Rebased use_python3.patch +- Drop python3 and perl build requirements, not needed, shbang of + executables can be patched anyway. + +------------------------------------------------------------------- Old: ---- bcftools-1.12.tar.bz2 New: ---- bcftools-1.15.1.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ bcftools.spec ++++++ --- /var/tmp/diff_new_pack.nGlyH5/_old 2022-05-04 15:11:05.764168000 +0200 +++ /var/tmp/diff_new_pack.nGlyH5/_new 2022-05-04 15:11:05.768168004 +0200 @@ -1,7 +1,7 @@ # # spec file for package bcftools # -# Copyright (c) 2021 SUSE LLC +# Copyright (c) 2022 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,7 +17,7 @@ Name: bcftools -Version: 1.12 +Version: 1.15.1 Release: 0 %define minor %(cut -d '.' -f 1,2 <<< %{version}) Summary: Tools for manipulating variant calls in the Variant Call Format (VCF) @@ -33,8 +33,6 @@ BuildRequires: libbz2-devel BuildRequires: libhts-devel >= %{minor} BuildRequires: lzma-devel -BuildRequires: perl -BuildRequires: python3-base BuildRequires: zlib-devel Requires: bgzip Requires: htsfile @@ -61,11 +59,8 @@ %make_install prefix=%{_prefix} libexecdir=%{_libdir} libdir=%{_libdir} # CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE -perlbin=`which perl` -sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/*.pl -sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/plot-vcfstats -pybin=`which python3` -sed -i -E "s:/usr/bin/env python3?:${pybin}:" %{buildroot}/%{_bindir}/*.py +sed -i "s:/usr/bin/env perl:%{_bindir}/perl:" %{buildroot}/%{_bindir}/*.pl %{buildroot}/%{_bindir}/plot-vcfstats +sed -i -E "s:/usr/bin/env python3?:%{_bindir}/python3:" %{buildroot}/%{_bindir}/*.py %files %license LICENSE ++++++ bcftools-1.12.tar.bz2 -> bcftools-1.15.1.tar.bz2 ++++++ /work/SRC/openSUSE:Factory/bcftools/bcftools-1.12.tar.bz2 /work/SRC/openSUSE:Factory/.bcftools.new.1538/bcftools-1.15.1.tar.bz2 differ: char 11, line 1 ++++++ use_python3.patch ++++++ --- /var/tmp/diff_new_pack.nGlyH5/_old 2022-05-04 15:11:05.804168048 +0200 +++ /var/tmp/diff_new_pack.nGlyH5/_new 2022-05-04 15:11:05.808168054 +0200 @@ -6,34 +6,34 @@ python3 compatible according to the documentation. This patch changes all the executables to use "python3" instead of "python". -diff -Nur bcftools-1.12/doc/bcftools.1 new/doc/bcftools.1 ---- bcftools-1.12/doc/bcftools.1 2021-03-17 10:16:18.000000000 +0100 -+++ new/doc/bcftools.1 2021-05-14 12:40:00.545719382 +0200 -@@ -5773,7 +5773,7 @@ - .nf +diff -Nur bcftools-1.15.1/doc/bcftools.1 new/doc/bcftools.1 +--- bcftools-1.15.1/doc/bcftools.1 2022-04-07 17:32:58.000000000 +0200 ++++ new/doc/bcftools.1 2022-04-21 17:54:28.011999739 +0200 +@@ -5841,7 +5841,7 @@ + .fam C # The final looks can be customized by editing the generated - # \*(Aqoutdir/plot\&.py\*(Aq script and re\-running manually --cd outdir && python plot\&.py && pdflatex summary\&.tex -+cd outdir && python3 plot\&.py && pdflatex summary\&.tex + # \*(Aqoutdir/plot.py\*(Aq script and re\-running manually +-cd outdir && python plot.py && pdflatex summary.tex ++cd outdir && python3 plot.py && pdflatex summary.tex + .fam .fi - .if n \{\ - .RE -diff -Nur bcftools-1.12/doc/bcftools.html new/doc/bcftools.html ---- bcftools-1.12/doc/bcftools.html 2021-03-17 10:16:18.000000000 +0100 -+++ new/doc/bcftools.html 2021-05-14 12:40:00.553719441 +0200 -@@ -3171,7 +3171,7 @@ - bcftools stats -s - > file.vchk</pre><pre class="literallayout"># Plot the stats - plot-vcfstats -p outdir file.vchk</pre><pre class="literallayout"># The final looks can be customized by editing the generated + .if n .RE +diff -Nur bcftools-1.15.1/doc/bcftools.html new/doc/bcftools.html +--- bcftools-1.15.1/doc/bcftools.html 2022-04-07 17:32:58.000000000 +0200 ++++ new/doc/bcftools.html 2022-04-21 17:54:28.011999739 +0200 +@@ -4942,7 +4942,7 @@ + <div class="content"> + <pre># The final looks can be customized by editing the generated # 'outdir/plot.py' script and re-running manually --cd outdir && python plot.py && pdflatex summary.tex</pre></div></div><div class="refsect1"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records -+cd outdir && python3 plot.py && pdflatex summary.tex</pre></div></div><div class="refsect1"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records - are internally converted into BCF representation. Simple operations, like removing - a single column from a VCF file, can be therefore done much faster with standard - UNIX commands, such as <span class="strong"><strong>awk</strong></span> or <span class="strong"><strong>cut</strong></span>. -diff -Nur bcftools-1.12/doc/bcftools.txt new/doc/bcftools.txt ---- bcftools-1.12/doc/bcftools.txt 2021-03-10 17:48:14.000000000 +0100 -+++ new/doc/bcftools.txt 2021-05-14 12:40:00.557719471 +0200 -@@ -3278,7 +3278,7 @@ +-cd outdir && python plot.py && pdflatex summary.tex</pre> ++cd outdir && python3 plot.py && pdflatex summary.tex</pre> + </div> + </div> + </div> +diff -Nur bcftools-1.15.1/doc/bcftools.txt new/doc/bcftools.txt +--- bcftools-1.15.1/doc/bcftools.txt 2022-03-03 16:10:50.000000000 +0100 ++++ new/doc/bcftools.txt 2022-04-21 17:54:28.011999739 +0200 +@@ -3635,7 +3635,7 @@ # The final looks can be customized by editing the generated # 'outdir/plot.py' script and re-running manually @@ -42,30 +42,18 @@ -- PERFORMANCE -diff -Nur bcftools-1.12/misc/guess-ploidy.py new/misc/guess-ploidy.py ---- bcftools-1.12/misc/guess-ploidy.py 2019-11-05 15:56:36.000000000 +0100 -+++ new/misc/guess-ploidy.py 2021-05-14 12:40:24.421895595 +0200 +diff -Nur bcftools-1.15.1/misc/guess-ploidy.py new/misc/guess-ploidy.py +--- bcftools-1.15.1/misc/guess-ploidy.py 2021-06-23 12:49:05.000000000 +0200 ++++ new/misc/guess-ploidy.py 2022-04-21 17:53:16.863999747 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python -+#!/usr/bin/python3 ++#!/usr/bin/env python3 # # Plot the output of "bcftools +guess-ploidy -v" # -diff -Nur bcftools-1.12/polysomy.c new/polysomy.c ---- bcftools-1.12/polysomy.c 2019-05-30 23:56:51.000000000 +0200 -+++ new/polysomy.c 2021-05-14 12:40:24.421895595 +0200 -@@ -253,7 +253,7 @@ - FILE *fp = open_file(&fname,"w","%s/dist.py", args->output_dir); - //-------- matplotlib script -------------- - fprintf(fp, -- "#!/usr/bin/env python\n" -+ "#!/usr/bin/python3\n" - "#\n" - "import matplotlib as mpl\n" - "mpl.use('Agg')\n" -diff -Nur bcftools-1.12/vcfcnv.c new/vcfcnv.c ---- bcftools-1.12/vcfcnv.c 2020-02-17 14:05:23.000000000 +0100 -+++ new/vcfcnv.c 2021-05-14 12:40:00.537719323 +0200 +diff -Nur bcftools-1.15.1/vcfcnv.c new/vcfcnv.c +--- bcftools-1.15.1/vcfcnv.c 2022-02-17 13:45:09.000000000 +0100 ++++ new/vcfcnv.c 2022-04-21 17:53:54.239999743 +0200 @@ -321,7 +321,7 @@ { if ( th>100 ) return; // create no plots
