[med-svn] [bcftools] 05/06: Refresh patches

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository bcftools.

commit 99ee7b13147f4768b38f1dfbf53bad62a1313d47
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jun 18 21:47:34 2017 +0200

    Refresh patches
---
 debian/patches/destdir.patch          |  8 ++++----
 debian/patches/external-libs.patch    | 34 +++++++++++++++++++---------------
 debian/patches/tests-pluginpath.patch |  8 ++++----
 3 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch
index 2687132..f524146 100644
--- a/debian/patches/destdir.patch
+++ b/debian/patches/destdir.patch
@@ -2,9 +2,9 @@ Description: Set installation prefix
 Author: Afif Elghraoui <afif at ghraoui.name>
 Forwarded: not-needed
 Last-Update: 2015-11-03
---- bcftools.orig/Makefile
-+++ bcftools/Makefile
-@@ -57,7 +57,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -70,7 +70,7 @@ ifdef USE_GPL
      GSL_LIBS = -lgsl -lgslcblas
  endif
  
@@ -13,7 +13,7 @@ Last-Update: 2015-11-03
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  libdir      = $(exec_prefix)/lib
-@@ -65,7 +65,7 @@
+@@ -78,7 +78,7 @@ libexecdir  = $(exec_prefix)/libexec
  mandir      = $(prefix)/share/man
  man1dir     = $(mandir)/man1
  
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index de0c3a1..a3f5f5f 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -2,17 +2,20 @@ Description: Use packaged libraries
 Author: Afif Elghraoui <afif at ghraoui.name>
 Forwarded: not-needed
 Last-Update: 2015-11-03
---- bcftools.orig/Makefile
-+++ bcftools/Makefile
-@@ -29,17 +29,14 @@
+--- 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
  
@@ -24,9 +27,9 @@ Last-Update: 2015-11-03
 +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 @@
+ 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
@@ -35,12 +38,13 @@ Last-Update: 2015-11-03
  endif
  
  prefix      = /usr/local
-@@ -101,10 +98,10 @@
+@@ -123,11 +117,11 @@ force:
  .c.o:
- 	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
+ 	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
  
--test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
-+test: $(PROG) plugins test/test-rbuf
+-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) $(TABIX)
@@ -48,14 +52,14 @@ Last-Update: 2015-11-03
  	./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
  
  
-@@ -180,8 +177,8 @@
- test/test-rbuf: test/test-rbuf.o
- 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
+@@ -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) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+-	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
 +bcftools: $(OBJS)
-+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
++	$(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
diff --git a/debian/patches/tests-pluginpath.patch b/debian/patches/tests-pluginpath.patch
index 6a71d97..1c88cdf 100644
--- a/debian/patches/tests-pluginpath.patch
+++ b/debian/patches/tests-pluginpath.patch
@@ -8,9 +8,9 @@ Description: Set the bcftools plugin path to search system directories
 Author: Afif Elghraoui <afif at ghraoui.name>
 Forwarded: not-needed
 Last-Update: 2015-11-09
---- bcftools.orig/test/test.pl
-+++ bcftools/test/test.pl
-@@ -776,7 +776,7 @@
+--- a/test/test.pl
++++ b/test/test.pl
+@@ -859,7 +859,7 @@ sub test_vcf_plugin
  {
      my ($opts,%args) = @_;
      if ( !$$opts{test_plugins} ) { return; }
@@ -18,4 +18,4 @@ Last-Update: 2015-11-09
 +    $ENV{BCFTOOLS_PLUGINS} = "$$opts{bin}/plugins:";
      if ( !exists($args{args}) ) { $args{args} = ''; }
      $args{args} =~ s/{PATH}/$$opts{path}/g;
-     bgzip_tabix_vcf($opts,"$args{in}");
+     $args{cmd}  =~ s/{PATH}/$$opts{path}/g;

-- 
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