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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 @@
# 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)
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