* Team upload.
* Incorporate patches from Ubuntu to fix FTBFS on some 32-bit archs.
* Fix autopkgtests by ensuring presence of all deps.
[dgit import unpatched bcftools 1.4.1-3]
--- /dev/null
--- /dev/null
++bcftools (1.4.1-3) unstable; urgency=medium
++
++ * Team upload.
++ * Incorporate patches from Ubuntu to fix FTBFS on some 32-bit archs.
++ * Fix autopkgtests by ensuring presence of all deps.
++
++ -- Sascha Steinbiss <satta@debian.org> Sat, 29 Jul 2017 10:38:27 +0200
++
++bcftools (1.4.1-2) unstable; urgency=medium
++
++ * Team upload
++ * Fix FTBFS on architectures where char is unsigned by default,
++ thanks Adrian Bunk (Closes: #865060)
++
++ -- Graham Inggs <ginggs@debian.org> Wed, 19 Jul 2017 11:00:08 +0200
++
++bcftools (1.4.1-1) unstable; urgency=medium
++
++ * Team upload
++ * New upstream version
++ Closes: #865006
++ * debhelper 10
++
++ -- Andreas Tille <tille@debian.org> Sun, 18 Jun 2017 21:41:36 +0200
++
++bcftools (1.3.1-1) unstable; urgency=medium
++
++ * Imported Upstream version 1.3.1
++ * Remove backported patches
++ * Refresh remaining patches
++ * Bump htslib minimum dependency
++ * Bump Standards-Version to 3.9.8
++ * Add a manpage for the color-chrs command
++
++ -- Afif Elghraoui <afif@debian.org> Mon, 25 Apr 2016 22:24:50 -0700
++
++bcftools (1.3-3) unstable; urgency=medium
++
++ * Backport upstream patch to fix build on arm64, armel, and ppc64el
++ (Closes: #812268)
++
++ -- Afif Elghraoui <afif@debian.org> Thu, 31 Mar 2016 00:57:18 -0700
++
++bcftools (1.3-2) unstable; urgency=medium
++
++ * Backport upstream patch to be able to build plugin with GSL2
++ * Bump Standards-Version
++ * Use encrypted protocols for VCS URLs
++
++ -- Afif Elghraoui <afif@ghraoui.name> Sun, 21 Feb 2016 16:35:44 -0800
++
++bcftools (1.3-1) unstable; urgency=medium
++
++ * New upstream release (Closes: #813465)
++ * Disable building with libgsl until build issue with GSL2 is addressed
++ * Update d/TODO to indicate GSL issue forwarded
++ * Simplify d/rules as a result of improvements to build system
++ * Update htslib minimum dependency
++ * Add libhts-dev dependency for CI tests
++
++ -- Afif Elghraoui <afif@ghraoui.name> Wed, 03 Feb 2016 23:44:03 -0800
++
++bcftools (1.2-2) unstable; urgency=medium
++
++ * Fix autopkgtest dependencies
++ * Declare conflict with older versions of samtools (Closes: #812328)
++
++ -- Afif Elghraoui <afif@ghraoui.name> Fri, 22 Jan 2016 18:52:53 -0800
++
++bcftools (1.2-1) unstable; urgency=low
++
++ * Initial release (Closes: #804007)
++
++ -- Afif Elghraoui <afif@ghraoui.name> Mon, 09 Nov 2015 23:44:39 -0800
--- /dev/null
--- /dev/null
++10
--- /dev/null
--- /dev/null
++Source: bcftools
++Section: science
++Priority: optional
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders:
++ Afif Elghraoui <afif@debian.org>
++Build-Depends:
++ debhelper (>= 10),
++ zlib1g-dev,
++ libhts-dev (>= 1.3.1),
++ libgsl-dev,
++# Test-Depends:
++ tabix,
++ libio-pty-perl
++Standards-Version: 3.9.8
++Homepage: http://samtools.github.io/bcftools/
++Vcs-Git: https://anonscm.debian.org/git/debian-med/bcftools.git
++Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bcftools.git
++
++Package: bcftools
++Architecture: any
++Breaks: samtools (<< 1.0)
++Replaces: samtools (<< 1.0)
++Depends:
++ ${shlibs:Depends},
++ ${misc:Depends},
++ ${perl:Depends}
++Suggests:
++# These are needed for plot-vcfstats
++ python,
++ python-numpy,
++ python-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
++ Variant Call Format (VCF) and its binary counterpart BCF. All commands work
++ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
--- /dev/null
--- /dev/null
++Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Name: bcftools
++Source: https://github.com/samtools/bcftools
++
++Files: *
++Copyright:
++ 2011-2015 Genome Research Ltd.
++ 2010-2012 Broad Institute
++License: MIT or GPL-3.0
++Comment:
++ Dual-licensing is in effect for the default compilation mode.
++ When linked with the GPL-licensed GNU Scientific Library
++ (as is done for this Debian package), the
++ resulting program must be distributed under the GPL.
++ .
++ The source distribution simply states "GPL-licensed" without indicating
++ a version of the GPL, but includes a copy of GPL-3.
++
++Files: kmin.*
++Copyright: 2008,2010 Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: debian/*
++Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
++License: MIT
++
++License: MIT
++ Permission is hereby granted, free of charge, to any person obtaining a
++ copy of this software and associated documentation files (the "Software"),
++ to deal in the Software without restriction, including without limitation
++ the rights to use, copy, modify, merge, publish, distribute, sublicense,
++ and/or sell copies of the Software, and to permit persons to whom the
++ Software is furnished to do so, subject to the following conditions:
++ .
++ The above copyright notice and this permission notice shall be included
++ in all copies or substantial portions of the Software.
++ .
++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
++ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
++ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
++ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
++ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
++ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
++ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
++
++License: GPL-3.0
++ This program is free software: you can redistribute it and/or modify
++ it under the terms of the GNU General Public License as published by
++ the Free Software Foundation.
++ .
++ This package is distributed in the hope that it will be useful,
++ but WITHOUT ANY WARRANTY; without even the implied warranty of
++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
++ GNU General Public License for more details.
++ .
++ You should have received a copy of the GNU General Public License
++ along with this program. If not, see <http://www.gnu.org/licenses/>.
++ .
++ On Debian systems, the complete text of the GNU General
++ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
--- /dev/null
--- /dev/null
++README
--- /dev/null
--- /dev/null
++.TH COLOR-CHRS.PL 1 "April 2016"
++.SH NAME
++color-chrs.pl \- Plot output of "bcftools +color-chrs"
++.SH SYNOPSIS
++.B color-chrs.pl
++.RI [ OPTIONS ]
++.I output.dat
++.SH OPTIONS
++.TP
++.B \-c, \-\-colors \f[I]file
++File with list of "chr hap color".
++.TP
++.B \-p, \-\-prefix \f[I]name
++Prefix of output files
++.TP
++.B \-h, \-?, \-\-help
++Summary of options.
++.SH SEE ALSO
++.BR bcftools (1)
--- /dev/null
--- /dev/null
++.TH PLOT-VCFSTATS 1 "November 2015"
++.SH NAME
++plot-vcfstats \- plot statistics for genomic variants in a VCF file
++.SH DESCRIPTION
++Call the program without any arguments for usage information.
++This program requires bcftools' suggested packages in order to function.
++See `apt-cache show bcftools` to see what the suggested packages are.
++.SH SEE ALSO
++.BR bcftools (1)
--- /dev/null
--- /dev/null
++.TH VCFUTILS.PL 1 "November 2015"
++.SH NAME
++vcfutils.pl \- utilities to manipulate files in the Variant Call Format (VCF)
++.SH DESCRIPTION
++Call the program with no arguments in order to see usage information.
++.SH SEE ALSO
++.BR bcftools (1)
--- /dev/null
--- /dev/null
++debian/man/*
--- /dev/null
--- /dev/null
++Description: Allow compiler flags to be passed through to build system
++ The development version of the upstream code already supports LDFLAGS,
++ so many parts of this patch will not be needed in the next upstream
++ release
++Author: Afif Elghraoui <afif@ghraoui.name>
++Forwarded: not-needed
++Last-Update: 2015-11-09
++--- bcftools.orig/Makefile
+++++ bcftools/Makefile
++@@ -32,9 +32,9 @@
++ BGZIP = /usr/bin/bgzip
++ TABIX = /usr/bin/tabix
++
++-CC = gcc
++-CPPFLAGS =
++-CFLAGS = -g -Wall -Wc++-compat -O2
+++CC ?= gcc
+++CPPFLAGS ?=
+++CFLAGS += -g -Wall -Wc++-compat -O2
++ LDFLAGS ?=
++ LIBS += $(LDFLAGS) -lhts
++
--- /dev/null
--- /dev/null
++Description: Set installation prefix
++Author: Afif Elghraoui <afif@ghraoui.name>
++Forwarded: not-needed
++Last-Update: 2015-11-03
++--- a/Makefile
+++++ b/Makefile
++@@ -70,7 +70,7 @@ ifdef USE_GPL
++ GSL_LIBS = -lgsl -lgslcblas
++ endif
++
++-prefix = /usr/local
+++prefix = /usr
++ exec_prefix = $(prefix)
++ bindir = $(exec_prefix)/bin
++ libdir = $(exec_prefix)/lib
++@@ -78,7 +78,7 @@ libexecdir = $(exec_prefix)/libexec
++ mandir = $(prefix)/share/man
++ man1dir = $(mandir)/man1
++
++-plugindir = $(libexecdir)/bcftools
+++plugindir ?= $(libexecdir)/bcftools
++ pluginpath = $(plugindir)
++
++ MKDIR_P = mkdir -p
--- /dev/null
--- /dev/null
++Description: Use packaged libraries
++Author: Afif Elghraoui <afif@ghraoui.name>
++Forwarded: not-needed
++Last-Update: 2015-11-03
++--- a/Makefile
+++++ b/Makefile
++@@ -29,20 +29,14 @@ TEST_PROG= test/test-rbuf test/test-reg
++ all: $(PROG) $(TEST_PROG)
++
++ # Adjust $(HTSDIR) to point to your top-level htslib directory
++-HTSDIR = ../htslib
++-include $(HTSDIR)/htslib.mk
++-include $(HTSDIR)/htslib_static.mk
++-HTSLIB = $(HTSDIR)/libhts.a
++-BGZIP = $(HTSDIR)/bgzip
++-TABIX = $(HTSDIR)/tabix
++-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
++-HTSLIB_LIBS = $(HTSLIB_static_LIBS)
+++BGZIP = /usr/bin/bgzip
+++TABIX = /usr/bin/tabix
++
++ CC = gcc
++ CPPFLAGS =
++ CFLAGS = -g -Wall -Wc++-compat -O2
++-LDFLAGS =
++-LIBS =
+++LDFLAGS ?=
+++LIBS += $(LDFLAGS) -lhts
++
++ ifeq "$(shell uname -s)" "Darwin"
++ DYNAMIC_FLAGS = -Wl,-export_dynamic
++@@ -73,7 +67,7 @@ GSL_LIBS =
++ ifdef USE_GPL
++ EXTRA_CPPFLAGS += -DUSE_GPL
++ OBJS += polysomy.o peakfit.o
++- GSL_LIBS = -lgsl -lcblas
+++ GSL_LIBS = -lgsl -lgslcblas
++ endif
++
++ prefix = /usr/local
++@@ -123,11 +117,11 @@ force:
++ .c.o:
++ $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
++
++-test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX)
+++test: $(PROG) plugins test/test-rbuf test/test-regidx
++ ./test/test-regidx
++ ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
++
++-test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
+++test-plugins: $(PROG) plugins test/test-rbuf
++ ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
++
++
++@@ -217,8 +211,8 @@ test/test-regidx.o: test/test-regidx.c r
++ test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
++ $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
++
++-bcftools: $(HTSLIB) $(OBJS)
++- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
+++bcftools: $(OBJS)
+++ $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
++
++ doc/bcftools.1: doc/bcftools.txt
++ cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
--- /dev/null
--- /dev/null
++Description: Fix buffer overflow
++Origin: upstream, https://github.com/samtools/bcftools/commit/8bfb9d5a94aaab4617bc38cfefa8332729dbd837
++Bug: https://github.com/samtools/bcftools/issues/607
++Bug-Debian: https://bugs.debian.org/868958
++Author: Petr Danecek <pd3@sanger.ac.uk>
++Last-Update: 2017-05-10
++--- a/filter.c
+++++ b/filter.c
++@@ -832,6 +832,7 @@
++ {
++ char *se = ss;
++ while ( *se && *se!=',' ) se++;
+++ hts_expand(double, i+1, tok->mvalues, tok->values);
++ if ( !*se ) tok->values[i] = strlen(ss);
++ else
++ {
--- /dev/null
--- /dev/null
++Description: Fix test_vcf_query on 32-bit architectures
++ Introduced by upstream commit:
++ https://github.com/samtools/bcftools/commit/25d042b833987d32e5de1fc3a109d357c4d0f738
++Forwarded: not-yet
++Bug-Debian: https://bugs.debian.org/868958
++Author: Graham Inggs <ginggs@debian.org>
++Last-Update 2017-07-21
++--- a/vcfnorm.c
+++++ b/vcfnorm.c
++@@ -94,7 +94,7 @@
++ }
++ static inline int has_non_acgtn(char *seq, int nseq)
++ {
++- char *end = nseq ? seq + nseq : seq + UINT32_MAX; // arbitrary large number
+++ char *end = nseq ? seq + nseq : seq + (UINT32_MAX >> 2); // arbitrary large number
++ while ( *seq && seq<end )
++ {
++ char c = toupper(*seq);
--- /dev/null
--- /dev/null
++external-libs.patch
++compiler-flags.patch
++destdir.patch
++tests-pluginpath.patch
++test-regidx-unsigned-char.patch
++fix-bufffer-overflow.patch
++fix-test_vcf_query.patch
--- /dev/null
--- /dev/null
++Description: Fix spelling errors
++Author: Afif Elghraoui <afif@ghraoui.name>
++Forwarded: no
++Last-Update: 2015-11-09
++--- bcftools.orig/doc/bcftools.1
+++++ bcftools/doc/bcftools.1
++@@ -546,7 +546,7 @@
++ .RE
++ .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
++ .sp
++-This command allows to add or remove annotations\&.
+++This command allows one to add or remove annotations\&.
++ .PP
++ \fB\-a, \-\-annotations\fR \fIfile\fR
++ .RS 4
++@@ -1041,7 +1041,7 @@
++ likelihood of novel mutation for constrained
++ \fB\-C\fR
++ \fItrio\fR
++-calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explictly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=\fIfloat\fR*exp(\-a\-b*len), where a=22\&.8689, b=0\&.2994 for insertions and a=21\&.9313, b=0\&.2856 for deletions [pubmed:23975140]\&. If only one value is given, the same mutation rate Pn is used for SNPs and indels\&.
+++calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=\fIfloat\fR*exp(\-a\-b*len), where a=22\&.8689, b=0\&.2994 for insertions and a=21\&.9313, b=0\&.2856 for deletions [pubmed:23975140]\&. If only one value is given, the same mutation rate Pn is used for SNPs and indels\&.
++ .RE
++ .PP
++ \fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
++@@ -2512,7 +2512,7 @@
++ // Longer description used by \*(Aqbcftools +name \-h\*(Aq
++ const char *usage(void);
++
++-// Called once at startup, allows to initialize local variables\&.
+++// Called once at startup, allows one to initialize local variables\&.
++ // Return 1 to suppress normal VCF/BCF header output, \-1 on critical
++ // errors, 0 otherwise\&.
++ int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
--- /dev/null
--- /dev/null
++Description: Fix test-regidx argument parsing on archs with unsigned char
++ On architectures where char is unsigned "c >= 0" was always true.
++Author: Adrian Bunk <bunk@debian.org>
++Bug-Debian: https://bugs.debian.org/865060
++
++--- a/test/test-regidx.c
+++++ b/test/test-regidx.c
++@@ -336,7 +336,7 @@
++ {"seed",1,0,'s'},
++ {0,0,0,0}
++ };
++- char c;
+++ int c;
++ int seed = (int)time(NULL);
++ while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0)
++ {
--- /dev/null
--- /dev/null
++Description: Set the bcftools plugin path to search system directories
++ The tests were intended to be run at build time only, so the test
++ script sets the plugins to be searched for /only/ in the build directory.
++ It does so by setting the environment variable BCFTOOLS_PLUGINS. However,
++ as described in the manpage bcftools(1), adding a colon to either side of
++ the path entry in the environment variable also searches the system
++ directories. We need this for autopkgtest to work.
++Author: Afif Elghraoui <afif@ghraoui.name>
++Forwarded: not-needed
++Last-Update: 2015-11-09
++--- a/test/test.pl
+++++ b/test/test.pl
++@@ -859,7 +859,7 @@ sub test_vcf_plugin
++ {
++ my ($opts,%args) = @_;
++ if ( !$$opts{test_plugins} ) { return; }
++- $ENV{BCFTOOLS_PLUGINS} = "$$opts{bin}/plugins";
+++ $ENV{BCFTOOLS_PLUGINS} = "$$opts{bin}/plugins:";
++ if ( !exists($args{args}) ) { $args{args} = ''; }
++ $args{args} =~ s/{PATH}/$$opts{path}/g;
++ $args{cmd} =~ s/{PATH}/$$opts{path}/g;
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++
++#DH_VERBOSE = 1
++#include /usr/share/dpkg/default.mk
++
++export HTSDIR=/usr/include
++export USE_GPL=1
++export plugindir=/usr/lib/$(DEB_HOST_MULTIARCH)/bcftools
++
++%:
++ dh $@ --parallel
++
++override_dh_installman:
++ dh_installman --language=C
--- /dev/null
--- /dev/null
++3.0 (quilt)
--- /dev/null
--- /dev/null
++Tests: runtests
++Depends:
++ @,
++ tabix,
++ perl,
++ @builddeps@
++Restrictions:
++ allow-stderr,
++ rw-build-tree,
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++
++export HTSDIR=/usr/include
++
++BGZIP=/usr/bin/bgzip
++TABIX=/usr/bin/tabix
++
++test: test/test-rbuf bcftools
++ ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
++
++bcftools:
++ ln -s /usr/bin/bcftools $@
++
++test/test-rbuf:
++ $(MAKE) $@
--- /dev/null
--- /dev/null
++version=3
++
++opts="filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/bcftools-$1.tar.gz/" \
++ https://github.com/samtools/bcftools/releases (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
projects / bcftools.git / commitdiff