[med-svn] [Git][med-team/allelecount][master] 10 commits: stabilise-makefiles.patch: new: fix --shuffle.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Mar 5 21:25:51 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / allelecount
Commits:
370af3bb by Étienne Mollier at 2026-03-05T21:54:29+01:00
stabilise-makefiles.patch: new: fix --shuffle.
Closes: #1105234
- - - - -
b2f86363 by Étienne Mollier at 2026-03-05T21:56:10+01:00
hardening.patch: normalize Last-Update time stamp.
- - - - -
c20e1336 by Étienne Mollier at 2026-03-05T21:57:13+01:00
d/watch: bump to Github uscan template version 5.
- - - - -
b716f512 by Étienne Mollier at 2026-03-05T22:20:54+01:00
perl-fixups.patch: new: fix heading, typos and style in manuals.
- - - - -
489604b2 by Étienne Mollier at 2026-03-05T22:20:59+01:00
d/control: add myself to uploaders.
- - - - -
9c1b5072 by Étienne Mollier at 2026-03-05T22:20:59+01:00
d/control: drop redundant Priority: optional.
- - - - -
26398671 by Étienne Mollier at 2026-03-05T22:20:59+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
b1c1dfa9 by Étienne Mollier at 2026-03-05T22:21:00+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
b82453cc by Étienne Mollier at 2026-03-05T22:24:49+01:00
d/lintian-overrides: delete: unused override.
- - - - -
25b2e246 by Étienne Mollier at 2026-03-05T22:25:30+01:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- − debian/lintian-overrides
- debian/patches/hardening.patch
- + debian/patches/perl-fixups.patch
- debian/patches/series
- + debian/patches/stabilise-makefiles.patch
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+allelecount (4.3.0-4) unstable; urgency=medium
+
+ * stabilise-makefiles.patch: new: fix --shuffle. (Closes: #1105234)
+ * hardening.patch: normalize Last-Update time stamp.
+ * d/watch: bump to Github uscan template version 5.
+ * perl-fixups.patch: new: fix heading, typos and style in manuals.
+ * d/control: add myself to uploaders.
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/lintian-overrides: delete: unused override.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 05 Mar 2026 22:25:20 +0100
+
allelecount (4.3.0-3) unstable; urgency=medium
* Build with make 4.4.1 (no-parallel)
=====================================
debian/control
=====================================
@@ -1,8 +1,8 @@
Source: allelecount
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Testsuite: autopkgtest-pkg-perl
Build-Depends: debhelper-compat (= 13),
libhts-dev,
@@ -17,11 +17,10 @@ Build-Depends: debhelper-compat (= 13),
libtest-fatal-perl <!nocheck>,
libtry-tiny-perl <!nocheck>,
perl
-Standards-Version: 4.7.0
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/allelecount
Vcs-Git: https://salsa.debian.org/med-team/allelecount.git
Homepage: https://github.com/cancerit/alleleCount
-Rules-Requires-Root: no
Package: allelecount
Architecture: any
=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-allelecount: script-with-language-extension usr/bin/*.*
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 May 2020 16:16:46 +0200
+Last-Update: 2020-05-11
Description: Propagate hardening flags
--- a/c/Makefile
=====================================
debian/patches/perl-fixups.patch
=====================================
@@ -0,0 +1,115 @@
+Description: fix manual pages.
+ These changes bring various fixes to the resulting manual pages from
+ perldoc: header, typos and style considerations.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2026-03-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- allelecount.orig/perl/lib/Sanger/CGP/AlleleCount/Genotype.pm
++++ allelecount/perl/lib/Sanger/CGP/AlleleCount/Genotype.pm
+@@ -21,6 +21,12 @@
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
+ ##########LICENCE##########
+
++=head1 NAME
++
++Sanger::CGP::AlleleCount::Genotype - Perl interface to alleleCounter
++
++=cut
++
+ use strict;
+
+ use Carp;
+@@ -40,6 +46,8 @@
+ const my $FLAG_REQ => 2;
+ const my $FLAG_FILT => 4+8+256+512+1024+2048; # 3852
+
++=over
++
+ =item new
+
+ Null constructor
+@@ -103,7 +111,7 @@
+
+ =item get_full_snp6_profile
+
+-Writes tab seperated allelic counts and depth to specified FH
++Writes tab separated allelic counts and depth to specified FH
+ Uses all snps defined in file used by ngs_cn (format slightly different)
+
+ =cut
+@@ -153,7 +161,7 @@
+
+ =item get_full_loci_profile
+
+-Writes tab seperated allelic counts and depth to specified FH
++Writes tab separated allelic counts and depth to specified FH
+ Uses all loci defined in specified file
+
+ =cut
+@@ -175,7 +183,10 @@
+
+ X N
+
++=back
++
+ =cut
++
+ sub gender_chk {
+ my ($self, $bam_file, $out_file, $loci_file, $min_pbq, $min_mapq, $fasta) = @_;
+ $self->configure($bam_file, $min_pbq, $min_mapq, $fasta);
+--- allelecount.orig/perl/lib/Sanger/CGP/AlleleCount/ToJson.pm
++++ allelecount/perl/lib/Sanger/CGP/AlleleCount/ToJson.pm
+@@ -21,6 +21,11 @@
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
+ ##########LICENCE##########
+
++=head1 NAME
++
++Sanger::CGP::AlleleCount::ToJson - Convert allele count file result format to JSON
++
++=cut
+
+ use strict;
+
+@@ -45,6 +50,8 @@
+ return $ALLELECOUNT_CONST{$item};
+ }
+
++=over
++
+ =item new
+
+ Null constructor
+@@ -62,6 +69,8 @@
+
+ Convert allele count file result format to JSON
+
++=back
++
+ =cut
+
+ sub alleleCountToJson{
+--- allelecount.orig/perl/bin/alleleCounter.pl
++++ allelecount/perl/bin/alleleCounter.pl
+@@ -93,7 +93,7 @@
+
+ =head1 NAME
+
+-alleleCounts.pl - Generate tab seperated file with allelic counts and depth for each specified locus.
++alleleCounts.pl - Generate tab separated file with allelic counts and depth for each specified locus.
+
+ =head1 SYNOPSIS
+
+--- allelecount.orig/perl/bin/alleleCounterToJson.pl
++++ allelecount/perl/bin/alleleCounterToJson.pl
+@@ -80,7 +80,7 @@
+
+ =head1 NAME
+
+-alleleCounterToJson.pl - Generate JSON format file from the tab seperated format
++alleleCounterToJson.pl - Generate JSON format file from the tab separated format
+
+ =head1 SYNOPSIS
+
=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
hardening.patch
+stabilise-makefiles.patch
+perl-fixups.patch
=====================================
debian/patches/stabilise-makefiles.patch
=====================================
@@ -0,0 +1,37 @@
+Description: stabilize c/Makefile recipes execution.
+ This change fixes build failures when running make with flag
+ --shuffle=reverse, resulting in error message:
+ .
+ /usr/bin/ld: cannot find ./src/bam_access.o: No such file or directory
+ .
+ which stems from missing the bin/ directory at a critical point.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1105234
+Forwarded: no
+Last-Update: 2026-03-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- allelecount.orig/c/Makefile
++++ allelecount/c/Makefile
+@@ -63,10 +63,10 @@
+
+ .NOTPARALLEL: test
+
+-all: clean make_bin make_htslib_tmp $(COUNTER_TARGET) test remove_htslib_tmp
++all: make_htslib_tmp $(COUNTER_TARGET) remove_htslib_tmp
+ @echo Binaries have been compiled.
+
+-$(COUNTER_TARGET): $(OBJS)
++$(COUNTER_TARGET): $(OBJS) bin
+ $(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
+
+ #Unit Tests
+@@ -79,7 +79,7 @@
+ coverage: CFLAGS += --coverage
+ coverage: test
+
+-make_bin:
++bin:
+ $(MD) ./bin
+
+ make_htslib_tmp:
=====================================
debian/watch
=====================================
@@ -1,4 +1,5 @@
-version=4
+Version: 5
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-https://github.com/cancerit/alleleCount/tags .*/v?@ANY_VERSION@\.tar\.gz
+Template: Github
+Project: alleleCount
+Owner: cancerit
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/2f80fef87eff6a9bff5fef35876ea8283a298c13...25b2e246e740e9a95feed77b99fed044be1fa316
--
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/2f80fef87eff6a9bff5fef35876ea8283a298c13...25b2e246e740e9a95feed77b99fed044be1fa316
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