Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package bcftools for openSUSE:Factory checked in at 2021-06-02 22:12:27 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/bcftools (Old) and /work/SRC/openSUSE:Factory/.bcftools.new.1898 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "bcftools" Wed Jun 2 22:12:27 2021 rev:2 rq:896936 version:1.12 Changes: -------- --- /work/SRC/openSUSE:Factory/bcftools/bcftools.changes 2020-02-25 16:05:01.560403638 +0100 +++ /work/SRC/openSUSE:Factory/.bcftools.new.1898/bcftools.changes 2021-06-02 22:12:57.336046968 +0200 @@ -1,0 +2,178 @@ +Fri May 14 10:42:08 UTC 2021 - Ferdinand Thiessen <r...@fthiessen.de> + +- Update to version 1.12 + * The output file type is determined from the output file name + suffix, where available, so the -O/--output-type option is often + no longer necessary. + * Make F_MISSING in filtering expressions work for sites with + multiple ALT alleles + * Fix N_PASS and F_PASS to behave according to expectation when + reverse logic is used (#1397). This fix has the side effect of + query (or programs like +trio-stats) behaving differently with + these expressions, operating now in site-oriented rather than + sample-oriented mode. + * bcftools annotate: + * New --rename-annots option to help fix broken VCFs + * New -C option allows to read a long list of options from a file + to prevent very long command lines. + * New append-missing logic allows annotations to be added for + each ALT allele in the same order as they appear in the VCF. + * bcftools concat: + * Do not phase genotypes by mistake if they are not already + phased with -l + * bcftools consensus: + * New --mask-with, --mark-del, --mark-ins, --mark-snv options + * Symbolic <DEL> should have only one REF base. If there are + multiple, take POS+1 as the first deleted base. + * Make consensus work when the first base of the reference genome + is deleted. + * bcftools +contrast: + * The NOVELGT annotation was previously not added when requested. + * bcftools convert: + * Make the --hapsample and --hapsample2vcf options consistent with + each other and with the documentation. + * bcftools call: + * Revamp of call -G, previously sample grouping by population was + not truly independent and could still be influenced by the + presence of other sample groups. + * Optional addition of INFO/PV4 annotation with call -a INFO/PV4 + * Remove generation of useless HOB and ICB annotation; + use +fill-tags -- -t HWE,ExcHet instead + * The call -f option was renamed to -a to (1) make it consistent + with mpileup and (2) to indicate that it includes both INFO and + FORMAT annotations + * bcftools csq: + * Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites + with too many per-sample consequences + * Fix a bug which incorrectly handled the --ncsq parameter and + could clash with reserved BCF values, consequently producing + truncated or even incorrect output of the %TBCSQ formatting + expression in bcftools query. + * bcftools +fill-tags: + * MAF definition revised for multiallelic sites, the second most + common allele is considered to be the minor allele + * New FORMAT/VAF, VAF1 annotations to set the fraction of + alternate reads provided FORMAT/AD is present + * bcftools gtcheck: + * support matching of a single sample against all other samples + in the file with -s qry:sample -s gt:-. + * bcftools merge: + * Make merge -R behavior consistent with other commands and pull + in overlapping records with POS outside of the regions + * Bug fix + * bcftools mpileup: + * Add new optional tag mpileup -a FORMAT/QS + * bcftools norm: + * New -a, --atomize functionality to decompose complex variants, + for example MNVs into consecutive SNVs + * New option --old-rec-tag to indicate the original variant + * bcftools query: + * Incorrect fields were printed in the per-sample output when + subset of samples was requested via -s/-S and the order of + samples in the header was different from the requested -s/-S order + * bcftools +prune: + * New options --random-seed and --nsites-per-win-mode + * bcftools +split-vep: + * Transcript selection now works also on the raw CSQ/BCSQ annotation. + * Bug fix, samples were dropped on VCF input and VCF/BCF output + * bcftools stats: + * Changes to QUAL and ts/tv plotting stats: avoid capping QUAL to + predefined bins, use an open-range logarithmic binning instead + * plot dual ts/tv stats: per quality bin and cumulative as if + threshold applied on the whole dataset + * bcftools +trio-dnm2: + * Major revamp of +trio-dnm plugin, which is now deprecated + and replaced by +trio-dnm2. + * The original trio-dnm calling model used genotype likelihoods + (PLs) as the input for calling. + * This new version also implements the DeNovoGear model. + * For more details see http://samtools.github.io/bcftools/trio-dnm.pdf +- Update use_python3.patch + +------------------------------------------------------------------- +Thu May 13 00:53:30 UTC 2021 - Ferdinand Thiessen <r...@fthiessen.de> + +- Update to version 1.11 + * Breaking change in -i/-e expressions on the FILTER column. + The new behaviour is: + Expression Result + FILTER="A" Exact match, for example "A;B" does not pass + FILTER!="A" Exact match, for example "A;B" does pass + FILTER~"A" Both "A" and "A;B" pass + FILTER!~"A" Neither "A" nor "A;B" pass + * Fix in commutative comparison operators, in some cases reversing + sides would produce incorrect results + * Better support for filtering on sample subsests + * bcftools annotate: + * Previously it was not possible to use --columns =TAG with INFO + tags and the --merge-logic feature was restricted to tab files + with BEG,END columns, now extended to work also with REF,ALT. + * Make annotate -TAG/+TAG work also with FORMAT fields. + * ID and FILTER can be transferred to INFO and ID can be populated + from INFO. + * bcftools consensus: + * Fix in handling symbolic deletions and overlapping variants. + * Fix --iupac-codes crash on REF-only positions with ALT=".". + * Fix --chain crash + * Preserve the case of the genome reference. + * Add new -a, --absent option which allows to set positions with + no supporting evidence to "N" (or any other character). + * bcftools convert: + * The option --vcf-ids now works also with -haplegendsample2vcf. + * New option --keep-duplicates + * bcftools csq: + * Add misc/gff2gff.py script for conversion between various + flavors of GFF files. The initial commit supports only one type + * Add missing consequence types. + * Allow overlapping CDS to support ribosomal slippage. + * bcftools +fill-tags: + * Added new annotations: INFO/END, TYPE, F_MISSING. + * bcftools filter: + * Make --SnpGap optionally filter also SNPs close to other variant + types. + * bcftools gtcheck: + * Complete revamp of the command. The new version is faster and allows + N:M sample comparisons, not just 1:N or NxN comparisons. Some + functionality was lost (plotting and clustering) but may be added back + on popular demand. + * bcftools +mendelian: + * Revamp of user options, output VCFs with mendelian errors annotation, + read PED files + * bcftools merge: + * Update headers when appropriate with the '--info-rules *:join' + INFO rule. + * Local alleles merging that produce LAA and LPL when requested, a + draft implementation of samtools/hts-specs#434 + * New --no-index which allows to merge unindexed files. + * Fixes in gVCF merging. + * bcftools norm: + * Fixes in --check-ref s reference setting features with non-ACGT bases. + * New --keep-sum switch to keep vector sum constant when splitting + multiallelics. + * bcftools +prune: + * Extend to allow annotating with various LD metrics: r^2, Lewontin's D' + * bcftools query: + * New %N_PASS() formatting expression to output the number of samples + that pass the filtering expression. + * bcftools reheader: + * Improved error reporting to prevent user mistakes. + * bcftools roh: + * The --AF-file description incorrectly suggested "REF\tALT" + instead of the correct "REF,ALT". + * RG lines could have negative length. + * new --include-noalt option to allow also ALT=. records. + * bcftools scatter: + * New plugin intended as a convenient inverse to concat + * bcftools +split: + * New --groups-file option for more flexibility of defining + desired output + * New --hts-opts option to reduce required memory by reusing + one output + header and allow overriding the default hFile's block size + * Add support for multisample output and sample renaming + * bcftools +split-vep: + * Add default types (Integer, Float, String) for VEP subfields + and make --columns - extract all subfields into INFO tags + in one go. + +------------------------------------------------------------------- Old: ---- bcftools-1.10.2.tar.bz2 New: ---- bcftools-1.12.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ bcftools.spec ++++++ --- /var/tmp/diff_new_pack.6kJJWl/_old 2021-06-02 22:12:57.944045464 +0200 +++ /var/tmp/diff_new_pack.6kJJWl/_new 2021-06-02 22:12:57.948045455 +0200 @@ -1,7 +1,7 @@ # # spec file for package bcftools # -# Copyright (c) 2020 SUSE LLC. +# Copyright (c) 2021 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,14 +12,14 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # Name: bcftools -Version: 1.10.2 -%define minor %(cut -d '.' -f 1,2 <<< %{version}) +Version: 1.12 Release: 0 +%define minor %(cut -d '.' -f 1,2 <<< %{version}) Summary: Tools for manipulating variant calls in the Variant Call Format (VCF) License: MIT Group: Productivity/Scientific/Other @@ -28,7 +28,7 @@ Source: https://github.com/samtools/bcftools/releases/download/%{version}/bcftools-%{version}.tar.bz2 # PATCH-FIX-OPENSUSE use_python3.patch -- Use python3 executable instead of python2 Patch0: use_python3.patch -BuildRequires: autoconf +BuildRequires: automake BuildRequires: gsl-devel BuildRequires: libbz2-devel BuildRequires: libhts-devel >= %{minor} @@ -53,8 +53,7 @@ %autosetup -p1 %build -autoheader -autoconf +autoreconf -fi %configure --with-htslib=system make USE_GSL=1 %{?_smp_mflags} @@ -66,7 +65,7 @@ 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 "s:/usr/bin/env python:${pybin}:" %{buildroot}/%{_bindir}/*.py +sed -i -E "s:/usr/bin/env python3?:${pybin}:" %{buildroot}/%{_bindir}/*.py %files %license LICENSE ++++++ bcftools-1.10.2.tar.bz2 -> bcftools-1.12.tar.bz2 ++++++ /work/SRC/openSUSE:Factory/bcftools/bcftools-1.10.2.tar.bz2 /work/SRC/openSUSE:Factory/.bcftools.new.1898/bcftools-1.12.tar.bz2 differ: char 11, line 1 ++++++ use_python3.patch ++++++ --- /var/tmp/diff_new_pack.6kJJWl/_old 2021-06-02 22:12:58.004045316 +0200 +++ /var/tmp/diff_new_pack.6kJJWl/_new 2021-06-02 22:12:58.004045316 +0200 @@ -6,11 +6,10 @@ python3 compatible according to the documentation. This patch changes all the executables to use "python3" instead of "python". - -diff -U 3 -H -w -E -d -r -N -- a/doc/bcftools.1 b/doc/bcftools.1 ---- a/doc/bcftools.1 -+++ b/doc/bcftools.1 -@@ -5440,7 +5440,7 @@ +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 # The final looks can be customized by editing the generated # \*(Aqoutdir/plot\&.py\*(Aq script and re\-running manually @@ -19,24 +18,22 @@ .fi .if n \{\ .RE - -diff -U 3 -H -w -E -d -r -N -- a/doc/bcftools.html b/doc/bcftools.html ---- a/doc/bcftools.html -+++ b/doc/bcftools.html -@@ -3012,7 +3012,7 @@ +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 # 'outdir/plot.py' script and re-running manually --cd outdir && python plot.py && pdflatex summary.tex</pre></div></div><div class="refsect1" title="PERFORMANCE"><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" title="PERFORMANCE"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records +-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 -U 3 -H -w -E -d -r -N -- a/doc/bcftools.txt b/doc/bcftools.txt ---- a/doc/bcftools.txt -+++ b/doc/bcftools.txt -@@ -3101,7 +3101,7 @@ +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 @@ # The final looks can be customized by editing the generated # 'outdir/plot.py' script and re-running manually @@ -45,10 +42,18 @@ -- PERFORMANCE - -diff -U 3 -H -w -E -d -r -N -- a/polysomy.c b/polysomy.c ---- a/polysomy.c -+++ b/polysomy.c +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 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/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 -------------- @@ -58,11 +63,10 @@ "#\n" "import matplotlib as mpl\n" "mpl.use('Agg')\n" - -diff -U 3 -H -w -E -d -r -N -- a/vcfcnv.c b/vcfcnv.c ---- a/vcfcnv.c -+++ b/vcfcnv.c -@@ -320,7 +320,7 @@ +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 +@@ -321,7 +321,7 @@ { if ( th>100 ) return; // create no plots @@ -71,16 +75,3 @@ int ret = system(cmd); if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd); free(cmd); - -diff -U 3 -H -w -E -d -r -N -- a/vcfgtcheck.c b/vcfgtcheck.c ---- a/vcfgtcheck.c -+++ b/vcfgtcheck.c -@@ -60,7 +60,7 @@ - { - mkdir_p(script); - int len = strlen(script); -- char *cmd = !strcmp(".py",script+len-3) ? msprintf("python %s", script) : msprintf("python %s.py", script); -+ char *cmd = !strcmp(".py",script+len-3) ? msprintf("python3 %s", script) : msprintf("python3 %s.py", script); - int ret = system(cmd); - if ( ret ) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd); - free(cmd);
