Initial import

1 files changed, 78 insertions, 0 deletions

diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
new file mode 100644
index 000000000000..737ab0d61d5d
--- /dev/null
+++ b/makefile-system-htslib.patch
@@ -0,0 +1,78 @@
+diff -aur bcftools-1.2/Makefile bcftools-1.2-patched/Makefile
+--- bcftools-1.2/Makefile	2015-02-02 16:40:17.000000000 +0100
++++ bcftools-1.2-patched/Makefile	2015-02-04 12:33:10.627010914 +0100
+@@ -29,11 +29,9 @@
+ all: $(PROG) $(TEST_PROG)
+ 
+ # Adjust $(HTSDIR) to point to your top-level htslib directory
+-HTSDIR = ../htslib
+-include $(HTSDIR)/htslib.mk
+-HTSLIB = $(HTSDIR)/libhts.a
+-BGZIP  = $(HTSDIR)/bgzip
+-TABIX  = $(HTSDIR)/tabix
++HTSDIR = /usr/include
++BGZIP  = bgzip
++TABIX  = tabix
+ 
+ CC       = gcc
+ CFLAGS   = -g -Wall -Wc++-compat -O2
+@@ -52,7 +50,7 @@
+ ifdef USE_GPL
+     CFLAGS += -DUSE_GPL
+     OBJS   += polysomy.o
+-    LDLIBS  = -lgsl -lcblas
++    LDLIBS  = -lgsl -lgslcblas
+ endif
+ 
+ prefix      = /usr/local
+@@ -90,10 +88,10 @@
+ .c.o:
+ 	$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+ 
+-test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
++test: $(PROG) plugins test/test-rbuf
+ 	./test/test.pl --exec bgzip=$(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)
+ 
+ 
+@@ -102,8 +100,8 @@
+ 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 +156,8 @@
+ test/test-rbuf: test/test-rbuf.o
+ 	$(CC) $(CFLAGS) -o $@ -lm -ldl $<
+ 
+-bcftools: $(HTSLIB) $(OBJS)
+-	$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
++bcftools: $(OBJS)
++	$(CC) $(CFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl -lhts $(LDLIBS)
+ 
+ doc/bcftools.1: doc/bcftools.txt
+ 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
+diff -aur bcftools-1.2/plugins/fixploidy.mk bcftools-1.2-patched/plugins/fixploidy.mk
+--- bcftools-1.2/plugins/fixploidy.mk	2015-02-02 16:40:17.000000000 +0100
++++ bcftools-1.2-patched/plugins/fixploidy.mk	2015-02-04 12:23:15.376535358 +0100
+@@ -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
+diff -aur bcftools-1.2/plugins/vcf2sex.mk bcftools-1.2-patched/plugins/vcf2sex.mk
+--- bcftools-1.2/plugins/vcf2sex.mk	2015-02-02 16:40:17.000000000 +0100
++++ bcftools-1.2-patched/plugins/vcf2sex.mk	2015-02-04 12:25:51.240884001 +0100
+@@ -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