[med-svn] [bcftools] 03/06: Update patches
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Feb 2 08:04:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository bcftools.
commit c84be00bde9085c93d4039133a90d9cfdce27a28
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Feb 1 20:31:11 2016 -0800
Update patches
---
debian/patches/compiler-flags.patch | 38 +----
debian/patches/destdir.patch | 17 +--
debian/patches/external-libs.patch | 57 +++-----
debian/patches/improve-plugin-support.patch | 212 ----------------------------
debian/patches/series | 1 -
debian/patches/spelling.patch | 28 +---
debian/patches/tests-pluginpath.patch | 2 +-
7 files changed, 34 insertions(+), 321 deletions(-)
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
index 69a8270..8623c25 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -7,44 +7,16 @@ Forwarded: not-needed
Last-Update: 2015-11-09
--- bcftools.orig/Makefile
+++ bcftools/Makefile
-@@ -32,8 +32,8 @@
+@@ -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
- DFLAGS =
- OBJS = main.o vcfindex.o tabix.o \
- vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
-@@ -52,6 +52,8 @@
- LDLIBS = -lgsl -lgslcblas
- endif
+ LDFLAGS ?=
+ LIBS += $(LDFLAGS) -lhts
-+LDLIBS += $(LDFLAGS)
-+
- prefix = /usr/local
- exec_prefix = $(prefix)
- bindir = $(exec_prefix)/bin
-@@ -100,7 +102,7 @@
- PLUGINM = $(PLUGINC:.c=.mk)
-
- %.so: %.c version.h version.c
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -lhts
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared $(LDFLAGS) -o $@ version.c $<
-
- -include $(PLUGINM)
-
---- bcftools.orig/plugins/fixploidy.mk
-+++ bcftools/plugins/fixploidy.mk
-@@ -1,2 +1,2 @@
- plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts $(LDFLAGS)
---- bcftools.orig/plugins/vcf2sex.mk
-+++ bcftools/plugins/vcf2sex.mk
-@@ -1,2 +1,2 @@
- plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts $(LDFLAGS)
diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch
index c50d542..83791ff 100644
--- a/debian/patches/destdir.patch
+++ b/debian/patches/destdir.patch
@@ -4,21 +4,12 @@ Forwarded: not-needed
Last-Update: 2015-11-03
--- bcftools.orig/Makefile
+++ bcftools/Makefile
-@@ -33,7 +33,7 @@
- TABIX = /usr/bin/tabix
-
- CC ?= gcc
--CFLAGS += -g -Wall -Wc++-compat -O2
-+CFLAGS += -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"$(pluginpath)\"
- DFLAGS =
- OBJS = main.o vcfindex.o tabix.o \
- vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
-@@ -54,7 +54,7 @@
-
- LDLIBS += $(LDFLAGS)
+@@ -57,7 +57,7 @@
+ GSL_LIBS = -lgsl -lgslcblas
+ endif
-prefix = /usr/local
+prefix = /usr
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
- mandir = $(prefix)/share/man
+ libdir = $(exec_prefix)/lib
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index 1fa717a..de0c3a1 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -4,7 +4,7 @@ Forwarded: not-needed
Last-Update: 2015-11-03
--- bcftools.orig/Makefile
+++ bcftools/Makefile
-@@ -29,11 +29,8 @@
+@@ -29,17 +29,14 @@
all: $(PROG) $(TEST_PROG)
# Adjust $(HTSDIR) to point to your top-level htslib directory
@@ -17,19 +17,27 @@ Last-Update: 2015-11-03
+TABIX = /usr/bin/tabix
CC = gcc
+ CPPFLAGS =
CFLAGS = -g -Wall -Wc++-compat -O2
-@@ -52,7 +49,7 @@
+-LDFLAGS =
+-LIBS =
++LDFLAGS ?=
++LIBS += $(LDFLAGS) -lhts
+
+ OBJS = main.o vcfindex.o tabix.o \
+ vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
+@@ -57,7 +54,7 @@
ifdef USE_GPL
- CFLAGS += -DUSE_GPL
- OBJS += polysomy.o
-- LDLIBS = -lgsl -lcblas
-+ LDLIBS = -lgsl -lgslcblas
+ EXTRA_CPPFLAGS += -DUSE_GPL
+ OBJS += polysomy.o peakfit.o
+- GSL_LIBS = -lgsl -lcblas
++ GSL_LIBS = -lgsl -lgslcblas
endif
prefix = /usr/local
-@@ -90,10 +87,10 @@
+@@ -101,10 +98,10 @@
.c.o:
- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+ $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
-test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
+test: $(PROG) plugins test/test-rbuf
@@ -40,39 +48,14 @@ Last-Update: 2015-11-03
./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
-@@ -102,8 +99,8 @@
- PLUGINS = $(PLUGINC:.c=.so)
- PLUGINM = $(PLUGINC:.c=.mk)
-
--%.so: %.c version.h version.c $(HTSDIR)/libhts.so
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
-+%.so: %.c version.h version.c
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -lhts
-
- -include $(PLUGINM)
-
-@@ -158,8 +155,8 @@
+@@ -180,8 +177,8 @@
test/test-rbuf: test/test-rbuf.o
- $(CC) $(CFLAGS) -o $@ -lm -ldl $<
+ $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
-bcftools: $(HTSLIB) $(OBJS)
-- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
+- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+bcftools: $(OBJS)
-+ $(CC) $(CFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl -lhts $(LDLIBS)
++ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
---- bcftools.orig/plugins/fixploidy.mk
-+++ bcftools/plugins/fixploidy.mk
-@@ -1,2 +1,2 @@
--plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
-+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
---- bcftools.orig/plugins/vcf2sex.mk
-+++ bcftools/plugins/vcf2sex.mk
-@@ -1,2 +1,2 @@
--plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
-+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
-+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
diff --git a/debian/patches/improve-plugin-support.patch b/debian/patches/improve-plugin-support.patch
deleted file mode 100644
index 2123b29..0000000
--- a/debian/patches/improve-plugin-support.patch
+++ /dev/null
@@ -1,212 +0,0 @@
-From bea7d08f1947df750acf2577dbe827b1a43f549b Mon Sep 17 00:00:00 2001
-From: John Marshall <jm18 at sanger.ac.uk>
-Date: Fri, 20 Mar 2015 11:03:58 +0000
-Subject: [PATCH] Update $BCFTOOLS_PLUGINS handling
-
-An empty entry in the environment variable means to search $(pluginpath)
-directories at that point; no environment variable set means search just
-those system directories. Document $BCFTOOLS_PLUGINS usage.
-
-Makefile installs plugins to $(plugindir), and allows both $(plugindir)
-and $(pluginpath) to be overridden if so desired. Fixes #204.
-https://github.com/samtools/bcftools/issues/204
----
- Makefile | 11 ++++++----
- doc/bcftools.1 | 16 ++++++++------
- doc/bcftools.html | 20 +++++++++++-------
- doc/bcftools.txt | 16 ++++++++++----
- vcfplugin.c | 62 +++++++++++++++++++++++++++++++++++--------------------
- 5 files changed, 81 insertions(+), 44 deletions(-)
-
---- bcftools.orig/doc/bcftools.1
-+++ bcftools/doc/bcftools.1
-@@ -2,12 +2,12 @@
- .\" Title: bcftools
- .\" Author: [see the "AUTHORS" section]
- .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
--.\" Date: 2015-01-21 15:01 GMT
-+.\" Date: 2015-03-20 11:57 GMT
- .\" Manual: \ \&
- .\" Source: \ \&
- .\" Language: English
- .\"
--.TH "BCFTOOLS" "1" "2015\-01\-21 15:01 GMT" "\ \&" "\ \&"
-+.TH "BCFTOOLS" "1" "2015\-03\-20 11:57 GMT" "\ \&" "\ \&"
- .\" -----------------------------------------------------------------
- .\" * Define some portability stuff
- .\" -----------------------------------------------------------------
-@@ -41,7 +41,7 @@
- BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
- .SS "VERSION"
- .sp
--This manual page was last updated \fB2015\-01\-21 15:01 GMT\fR and refers to bcftools git version \fB1\&.1\-140\-g9b0e7cc+\fR\&.
-+This manual page was last updated \fB2015\-03\-20 11:57 GMT\fR and refers to bcftools git version \fB1\&.2\-6\-ga8d7fe9+\fR\&.
- .SS "BCF1"
- .sp
- The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
-@@ -1918,9 +1918,13 @@
- .PP
- \fB\-l, \-\-list\-plugins\fR
- .RS 4
--List all available plugins\&. If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include directory where
--\fBlibhts\&.so\fR
--is located\&. The BCFTOOLS_PLUGINS environment variable tells the program which directories to search\&.
-+List all available plugins\&.
-+.sp
-+By default, appropriate system directories are searched for installed plugins\&. You can override this by setting the BCFTOOLS_PLUGINS environment variable to a colon\-separated list of directories to search\&. If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains adjacent colons, the system directories are also searched at that position in the list of directories\&.
-+.sp
-+If htslib is not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the directory where
-+\fBlibhts\&.so\&.1\fR
-+is located\&.
- .RE
- .PP
- \fB\-v, \-\-verbose\fR
---- bcftools.orig/doc/bcftools.html
-+++ bcftools/doc/bcftools.html
-@@ -1,13 +1,13 @@
- <?xml version="1.0" encoding="UTF-8"?>
- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
--<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25137184"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manip [...]
-+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp135936"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipul [...]
- Call Format (VCF) and its binary counterpart BCF. All commands work
- transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
- automatically even when streaming from a pipe. Indexed VCF and BCF
- will work in all situations. Un-indexed VCF and BCF and streams will
- work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
- standard input (stdin) and outputs to the standard output (stdout). Several
--commands can thus be combined with Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-01-21 15:01 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.1-140-g9b0e7cc+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools <= 0.1.19 is <span class="strong" [...]
-+commands can thus be combined with Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-03-20 11:57 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-6-ga8d7fe9+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools <= 0.1.19 is <span class="strong">< [...]
- compatible with this version of bcftools. To read BCF1 files one can use
- the view command from old versions of bcftools packaged with samtools
- versions <= 0.1.19 to convert to VCF, which can then be read by
-@@ -1059,12 +1059,16 @@
- list plugin’s options
- </dd><dt><span class="term">
- <span class="strong"><strong>-l, --list-plugins</strong></span>
--</span></dt><dd>
-- List all available plugins. If not installed systemwide, set the environment
-- variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include
-- directory where <span class="strong"><strong>libhts.so</strong></span> is located. The BCFTOOLS_PLUGINS
-- environment variable tells the program which directories to search.
--</dd><dt><span class="term">
-+</span></dt><dd><p class="simpara">
-+ List all available plugins.
-+</p><p class="simpara">By default, appropriate system directories are searched for installed plugins.
-+ You can override this by setting the BCFTOOLS_PLUGINS environment variable
-+ to a colon-separated list of directories to search.
-+ If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
-+ adjacent colons, the system directories are also searched at that position
-+ in the list of directories.</p><p class="simpara">If htslib is not installed systemwide, set the environment variable
-+ LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the
-+ directory where <span class="strong"><strong>libhts.so.1</strong></span> is located.</p></dd><dt><span class="term">
- <span class="strong"><strong>-v, --verbose</strong></span>
- </span></dt><dd>
- print debugging information to debug plugin failure
---- bcftools.orig/doc/bcftools.txt
-+++ bcftools/doc/bcftools.txt
-@@ -1103,10 +1103,18 @@
- list plugin's options
-
- *-l, --list-plugins*::
-- List all available plugins. If not installed systemwide, set the environment
-- variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include
-- directory where *libhts.so* is located. The BCFTOOLS_PLUGINS
-- environment variable tells the program which directories to search.
-+ List all available plugins.
-++
-+By default, appropriate system directories are searched for installed plugins.
-+ You can override this by setting the BCFTOOLS_PLUGINS environment variable
-+ to a colon-separated list of directories to search.
-+ If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
-+ adjacent colons, the system directories are also searched at that position
-+ in the list of directories.
-++
-+If htslib is not installed systemwide, set the environment variable
-+ LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the
-+ directory where *libhts.so.1* is located.
-
- *-v, --verbose*::
- print debugging information to debug plugin failure
---- bcftools.orig/vcfplugin.c
-+++ bcftools/vcfplugin.c
-@@ -146,30 +146,55 @@
-
- char *msprintf(const char *fmt, ...);
-
--static void init_plugin_paths(args_t *args)
-+static void add_plugin_paths(args_t *args, const char *path)
- {
-- if ( args->nplugin_paths!=-1 ) return;
--
-- char *path = getenv("BCFTOOLS_PLUGINS");
-- if ( path )
-+ while (1)
- {
-- args->nplugin_paths = 1;
-- args->plugin_paths = (char**) malloc(sizeof(char*));
-- char *ss = args->plugin_paths[0] = strdup(path);
-- while ( *ss )
-+ size_t len = strcspn(path, ":");
-+
-+ if ( len == 0 )
- {
-- if ( *ss==':' )
-+#ifdef PLUGINPATH
-+ add_plugin_paths(args, PLUGINPATH);
-+#endif
-+ }
-+ else
-+ {
-+ char *dir = (char *) malloc(len + 1);
-+ strncpy(dir, path, len);
-+ dir[len] = '\0';
-+
-+ struct stat st;
-+ if ( stat(dir, &st) == 0 )
- {
-- *ss = 0;
- args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1));
-- args->plugin_paths[args->nplugin_paths] = ss+1;
-+ args->plugin_paths[args->nplugin_paths] = dir;
- args->nplugin_paths++;
-+ if ( args->verbose ) fprintf(stderr, "plugin directory %s .. ok\n", dir);
- }
-- ss++;
-+ else
-+ {
-+ if ( args->verbose ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
-+ free(dir);
-+ }
-+
- }
-+
-+ path += len;
-+ if ( *path == ':' ) path++;
-+ else break;
- }
-- else
-- args->nplugin_paths = 0;
-+}
-+
-+static void init_plugin_paths(args_t *args)
-+{
-+ if ( args->nplugin_paths!=-1 ) return;
-+
-+ args->nplugin_paths = 0;
-+ args->plugin_paths = NULL;
-+
-+ char *path = getenv("BCFTOOLS_PLUGINS");
-+ add_plugin_paths(args, path ? path : "");
- }
-
- static void *dlopen_plugin(args_t *args, const char *fname)
-@@ -410,7 +435,8 @@
- if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
- if ( args->nplugin_paths>0 )
- {
-- free(args->plugin_paths[0]);
-+ int i;
-+ for (i=0; i<args->nplugin_paths; i++) free(args->plugin_paths[i]);
- free(args->plugin_paths);
- }
- if ( args->filter )
diff --git a/debian/patches/series b/debian/patches/series
index 14aee1b..89d3d83 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-improve-plugin-support.patch
external-libs.patch
compiler-flags.patch
destdir.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 538a3f9..296c042 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -4,8 +4,8 @@ Forwarded: no
Last-Update: 2015-11-09
--- bcftools.orig/doc/bcftools.1
+++ bcftools/doc/bcftools.1
-@@ -465,7 +465,7 @@
- .\}
+@@ -546,7 +546,7 @@
+ .RE
.SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
.sp
-This command allows to add or remove annotations\&.
@@ -13,7 +13,7 @@ Last-Update: 2015-11-09
.PP
\fB\-a, \-\-annotations\fR \fIfile\fR
.RS 4
-@@ -779,7 +779,7 @@
+@@ -1041,7 +1041,7 @@
likelihood of novel mutation for constrained
\fB\-C\fR
\fItrio\fR
@@ -22,7 +22,7 @@ Last-Update: 2015-11-09
.RE
.PP
\fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
-@@ -2123,7 +2123,7 @@
+@@ -2512,7 +2512,7 @@
// Longer description used by \*(Aqbcftools +name \-h\*(Aq
const char *usage(void);
@@ -31,23 +31,3 @@ Last-Update: 2015-11-09
// 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);
---- bcftools.orig/vcfcall.c
-+++ bcftools/vcfcall.c
-@@ -169,7 +169,7 @@
- sam = add_sample(sam, &n, &max, col_ends[0]+1, ploidy, &j);
- if ( strcmp(col_ends[1]+1,"0") ) // father
- {
-- if ( fam->sample[CHILD]>=0 ) error("Multiple childs in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
-+ if ( fam->sample[CHILD]>=0 ) error("Multiple children in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
- fam->sample[CHILD] = j;
- if ( fam->sample[FATHER]>=0 ) error("Two fathers in %s?\n", str.s);
- sam = add_sample(sam, &n, &max, col_ends[1]+1, call->flag & (CALL_CHR_X|CALL_CHR_Y) ? 1 : 2, &fam->sample[FATHER]);
-@@ -189,7 +189,7 @@
- }
- assert( n==_n );
- for (i=0; i<call->nfams; i++)
-- assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple childs, not a trio
-+ assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple children, not a trio
-
- return sam;
- }
diff --git a/debian/patches/tests-pluginpath.patch b/debian/patches/tests-pluginpath.patch
index 9b36d4a..84ba9dc 100644
--- a/debian/patches/tests-pluginpath.patch
+++ b/debian/patches/tests-pluginpath.patch
@@ -10,7 +10,7 @@ Forwarded: not-needed
Last-Update: 2015-11-09
--- bcftools.orig/test/test.pl
+++ bcftools/test/test.pl
-@@ -689,7 +689,7 @@
+@@ -760,7 +760,7 @@
{
my ($opts,%args) = @_;
if ( !$$opts{test_plugins} ) { return; }
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git
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