diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-1.3-buildsystem.patch')
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.3-buildsystem.patch | 174 |
1 files changed, 0 insertions, 174 deletions
diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch deleted file mode 100644 index 61f6b03bd8ef..000000000000 --- a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch +++ /dev/null @@ -1,174 +0,0 @@ ---- 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) |