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|
--- samtools-1.3/Makefile
+++ samtools-1.3/Makefile
@@ -21,11 +21,12 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -O2
-LDFLAGS =
-LIBS =
+CC ?= gcc
+CPPFLAGS +=
+CFLAGS ?= -g -Wall -O2
+LDFLAGS +=
+LIBS +=
+BAMLIB ?= libbam.a
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
LOBJS= bam_aux.o bam.o bam_import.o sam.o \
@@ -42,6 +43,7 @@
prefix = /usr/local
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
+libdir ?= $(exec_prefix)/lib
datarootdir = $(prefix)/share
mandir = $(datarootdir)/man
man1dir = $(mandir)/man1
@@ -129,67 +131,74 @@
.c.o:
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+$(LOBJS):
+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
-lib:libbam.a
+lib:libbam.a libbam.so.1.0
libbam.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
-samtools: $(AOBJS) libbam.a $(HTSLIB)
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS)
+libbam.so.1.0:$(LOBJS)
+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
+ ln -sf $@ libbam.so.1
+ ln -sf $@ libbam.so
+
+samtools: $(AOBJS) lib
+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h)
sam_h = sam.h $(htslib_sam_h) $(bam_h)
sam_opts_h = sam_opts.h $(htslib_hts_h)
-sample_h = sample.h $(htslib_kstring_h)
+sample_h = sample.h
bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h
-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h
+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h)
bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h)
bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
bam_aux.o: bam_aux.c $(bam_h)
bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h)
bam_color.o: bam_color.c $(bam_h)
-bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
+bam_import.o: bam_import.c $(bam_h)
+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h)
+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h)
bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h)
bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h)
bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h)
bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
-bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h)
-bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h)
-bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h)
+bam_rmdup.o: bam_rmdup.c $(sam_h)
+bam_rmdupse.o: bam_rmdupse.c $(sam_h)
+bam_sort.o: bam_sort.c $(htslib_sam_h)
bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h)
bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h
bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h)
bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
bam_flags.o: bam_flags.c $(htslib_sam_h)
-bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h
-bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
-bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
+bedcov.o: bedcov.c $(htslib_sam_h)
+bedidx.o: bedidx.c
cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h)
dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h)
-errmod.o: errmod.c errmod.h $(htslib_ksort_h)
+errmod.o: errmod.c errmod.h
kprobaln.o: kprobaln.c kprobaln.h
padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h)
-phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
+phase.o: phase.c $(htslib_sam_h) errmod.h
sam.o: sam.c $(htslib_faidx_h) $(sam_h)
-sam_header.o: sam_header.c sam_header.h $(htslib_khash_h)
+sam_header.o: sam_header.c sam_header.h
sam_opts.o: sam_opts.c $(sam_opts_h)
-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
-sample.o: sample.c $(sample_h) $(htslib_khash_h)
-stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h)
-stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h
+sample.o: sample.c $(sample_h)
+stats_isize.o: stats_isize.c stats_isize.h
+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h)
# test programs
@@ -197,8 +206,8 @@
# 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 +219,28 @@
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
$(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
$(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
$(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
$(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
$(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
$(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
$(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)
|
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