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--- samtools-1.3.1/Makefile.ori 2016-04-22 11:51:16.000000000 +0200
+++ samtools-1.3.1/Makefile 2017-02-16 23:41:19.819951687 +0100
@@ -21,9 +21,9 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
+CC ?= gcc
CPPFLAGS =
-CFLAGS = -g -Wall -O2
+CFLAGS ?= -g -Wall -O2
LDFLAGS =
LIBS =
@@ -197,8 +203,8 @@
# 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) $(BUILT_TEST_PROGRAMS)
- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
+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_rtrans_build
test/merge/test_trans_tbl_init
@@ -210,28 +216,28 @@
test/split/test_parse_args
-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB)
+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB)
+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB)
+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB)
+test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB)
+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB)
+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB)
+test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
+test/vcf-miniview: test/vcf-miniview.o
$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS)
test_test_h = test/test.h $(htslib_sam_h)
@@ -258,10 +264,10 @@
misc/maq2sam-long: misc/maq2sam-long.o
$(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
-misc/md5fa: misc/md5fa.o $(HTSLIB)
+misc/md5fa: misc/md5fa.o
$(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
-misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
+misc/md5sum-lite: misc/md5sum-lite.o
$(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
misc/wgsim: misc/wgsim.o
|
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