Andreas Tille pushed to branch master at Debian Med / bcftools
Commits:
a46c2e25 by Andreas Tille at 2024-04-18T16:34:52+02:00
Add missing Depends
- - - - -
f9ef9e75 by Andreas Tille at 2024-04-18T16:35:07+02:00
routine-update: Standards-Version: 4.7.0
- - - - -
c413305a by Andreas Tille at 2024-04-18T17:14:25+02:00
Refresh patches
- - - - -
f2576d2a by Andreas Tille at 2024-04-18T17:19:00+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/skip_new_test_failing_on_32bit.patch
- debian/patches/tests-pluginpath.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,15 @@
-bcftools (1.20-1) UNRELEASED; urgency=medium
+bcftools (1.20-1) unstable; urgency=medium
+ [ Charles Plessy ]
* Team upload.
* New upstream version
- -- Charles Plessy <ple...@debian.org> Thu, 18 Apr 2024 08:51:21 +0900
+ [ Andreas Tille ]
+ * Add missing Depends
+ Closes: #1069234
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <ti...@debian.org> Thu, 18 Apr 2024 17:14:39 +0200
bcftools (1.19-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libgsl-dev,
tabix <!nocheck>,
libio-pty-perl <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/bcftools
Vcs-Git: https://salsa.debian.org/med-team/bcftools.git
Homepage: https://samtools.github.io/bcftools/
@@ -22,13 +22,14 @@ Package: bcftools
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- sse2-support [i386]
+ sse2-support [i386],
+ python3-gffutils,
+ python3-matplotlib
Recommends: perl
Suggests:
# These are needed for plot-vcfstats
python3,
python3-numpy,
- python3-matplotlib,
texlive-latex-recommended
Description: genomic variant calling and manipulation of VCF/BCF files
BCFtools is a set of utilities that manipulate variant calls in the
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
tests-pluginpath.patch
skip_new_test_failing_on_32bit.patch
2to3.patch
-typo.patch
=====================================
debian/patches/skip_new_test_failing_on_32bit.patch
=====================================
@@ -9,9 +9,9 @@ Description: Skip single test causing new failures
.
FIXME: This workaround needs to be reconsidered in future versions
---- bcftools.orig/test/test.pl
-+++ bcftools/test/test.pl
-@@ -206,7 +206,7 @@
+--- a/test/test.pl
++++ b/test/test.pl
+@@ -212,7 +212,7 @@ run_test(\&test_vcf_query,$opts,in=>'que
run_test(\&test_vcf_query,$opts,in=>'query.filter.11',out=>'query.81.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GT\\n]'
-e'N_PASS(GT="alt")==1']);
run_test(\&test_vcf_query,$opts,in=>'query.filter.11',out=>'query.80.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GT\\n]'
-e'N_PASS(GT="alt")!=1']);
run_test(\&test_vcf_query,$opts,in=>'query',out=>'query.64.out',args=>q[-f'%CHROM\\t%POS\\t%INFO\\t%FORMAT\\n'
-s D,C]);
=====================================
debian/patches/tests-pluginpath.patch
=====================================
@@ -8,9 +8,9 @@ Description: Set the bcftools plugin path to search system
directories
Author: Afif Elghraoui <a...@ghraoui.name>
Forwarded: not-needed
Last-Update: 2015-11-09
---- bcftools.orig/test/test.pl
-+++ bcftools/test/test.pl
-@@ -1742,7 +1742,7 @@
+--- a/test/test.pl
++++ b/test/test.pl
+@@ -1811,7 +1811,7 @@ sub test_vcf_plugin
{
my ($opts,%args) = @_;
if ( !$$opts{test_plugins} ) { return; }
View it on GitLab:
https://salsa.debian.org/med-team/bcftools/-/compare/0590dca4fe5ed1591d7a44fc573eb09199444bef...f2576d2a782334295689fe9c1d93c4ac97c287c8
--
View it on GitLab:
https://salsa.debian.org/med-team/bcftools/-/compare/0590dca4fe5ed1591d7a44fc573eb09199444bef...f2576d2a782334295689fe9c1d93c4ac97c287c8
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