1 files changed, 8 insertions, 91 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
index 864ac22bc7a6..bd46ac328d44 100644
--- a/makefile-system-htslib.patch
+++ b/makefile-system-htslib.patch
@@ -1,96 +1,13 @@
 diff -aur samtools-1.2/Makefile samtools-1.2-patched/Makefile
 --- samtools-1.2/Makefile	2015-02-02 16:18:41.000000000 +0100
-+++ samtools-1.2-patched/Makefile	2015-02-04 11:58:14.059908160 +0100
-@@ -25,7 +25,7 @@
- CPPFLAGS = $(DFLAGS) $(INCLUDES)
- CFLAGS   = -g -Wall -O2
- LDFLAGS  =
--LDLIBS   =
-+LDLIBS   = -lhts
- DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-             sam_header.o bam_plbuf.o
-@@ -82,10 +82,8 @@
- 
++++ samtools-1.2-patched/Makefile	2015-06-30 15:48:41.006563956 +0200
+@@ -83,7 +83,9 @@
  
  # Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = ../htslib
--include $(HTSDIR)/htslib.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP  = $(HTSDIR)/bgzip
-+HTSDIR = /usr/include
-+BGZIP  = bgzip
- 
- 
- PACKAGE_VERSION = 1.2
-@@ -121,8 +119,8 @@
- libbam.a:$(LOBJS)
- 	$(AR) -csru $@ $(LOBJS)
- 
--samtools: $(AOBJS) libbam.a $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
-+samtools: $(AOBJS) libbam.a
-+	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(LDLIBS) $(LIBCURSES) -lm -lz
- 
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
-@@ -178,7 +176,7 @@
- # For tests that might use it, set $REF_PATH explicitly to use only reference
- # areas within the test suite (or set it to ':' to use no reference areas).
- # (regression.sh sets $REF_PATH to a subdirectory itself.)
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
-+check test: samtools $(BUILT_TEST_PROGRAMS)
- 	REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
- 	test/merge/test_bam_translate test/merge/test_bam_translate.tmp
- 	test/merge/test_pretty_header
-@@ -191,32 +189,32 @@
- 	test/split/test_parse_args
- 
- 
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(LDLIBS) -lz
- 
--test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_pretty_header: test/merge/test_pretty_header.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(LDLIBS) -lz
- 
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(LDLIBS) -lz
- 
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(LDLIBS) -lz
- 
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(LDLIBS) -lz
- 
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(LDLIBS) -lz
- 
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(LDLIBS) -lz
- 
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(LDLIBS) -lz
- 
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
--	$(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz
-+test/vcf-miniview: test/vcf-miniview.o
-+	$(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(LDLIBS) -lz
- 
- test_test_h = test/test.h $(htslib_sam_h)
+ HTSDIR = ../htslib
++ifneq ("$(wildcard $(HTSDIR)/htslib.mk)","")
+ include $(HTSDIR)/htslib.mk
++endif
+ HTSLIB = $(HTSDIR)/libhts.a
+ BGZIP  = $(HTSDIR)/bgzip