diff options
Diffstat (limited to 'makefile-system-htslib.patch')
| -rw-r--r-- | makefile-system-htslib.patch | 79 |
1 files changed, 13 insertions, 66 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch index 91056165a424..7ae2b4c6f295 100644 --- a/makefile-system-htslib.patch +++ b/makefile-system-htslib.patch @@ -1,16 +1,18 @@ ---- /tmp/bcftools-1.3/Makefile 2015-12-15 22:58:35.000000000 +0100 -+++ /tmp/makepkg/bcftools/src/bcftools-1.3/Makefile 2016-03-05 11:24:58.512091814 +0100 -@@ -28,18 +28,8 @@ +diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile +--- /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile 2016-04-22 11:50:59.000000000 +0200 ++++ /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile 2016-05-29 20:18:22.323268586 +0200 +@@ -28,18 +28,10 @@ all: $(PROG) $(TEST_PROG) -# Adjust $(HTSDIR) to point to your top-level htslib directory --HTSDIR = htslib-1.3 +-HTSDIR = htslib-1.3.1 -include $(HTSDIR)/htslib.mk -HTSLIB = $(HTSDIR)/libhts.a -BGZIP = $(HTSDIR)/bgzip -TABIX = $(HTSDIR)/tabix -- ++HTSDIR = /usr/include + CC = gcc -CPPFLAGS = -CFLAGS = -g -Wall -Wc++-compat -O2 @@ -20,7 +22,7 @@ OBJS = main.o vcfindex.o tabix.o \ vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \ -@@ -48,7 +38,7 @@ +@@ -48,7 +40,7 @@ vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling @@ -29,7 +31,7 @@ GSL_LIBS = # The polysomy command is not compiled by default because it brings dependency -@@ -57,7 +47,7 @@ +@@ -57,7 +49,7 @@ ifdef USE_GPL EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o @@ -38,7 +40,7 @@ endif prefix = /usr/local -@@ -101,11 +91,11 @@ +@@ -101,11 +93,11 @@ .c.o: $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $< @@ -54,64 +56,7 @@ # Plugin rules -@@ -136,20 +126,20 @@ - filter_h = filter.h $(htslib_vcf_h) - ploidy_h = ploidy.h $(htslib_regidx_h) - prob1_h = prob1.h $(htslib_vcf_h) $(call_h) --roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) -+roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) - cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) - - main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) --vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) --vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) --vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) --vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) -+vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) vcmp.h $(filter_h) -+vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) vcmp.h $(filter_h) -+vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) -+vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) - vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) - vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h - vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) - vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) - vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) --vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h -+vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h - vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h - vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) - vcfroh.o: vcfroh.c $(roh_h) -@@ -157,22 +147,22 @@ - vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) - vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) - vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) --reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) -+reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(bcftools_h) - tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) --ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) -+ccall.o: ccall.c $(call_h) kmin.h $(prob1_h) - convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) - tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) - em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) --filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) -+filter.o: filter.c $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) - gvcf.o: gvcf.c $(call_h) - kmin.o: kmin.c kmin.h --mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) -+mcall.o: mcall.c $(call_h) - prob1.o: prob1.c $(prob1_h) - vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h --ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) -+ploidy.o: ploidy.c $(htslib_regidx_h) $(htslib_hts_h) $(bcftools_h) $(ploidy_h) - polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h --peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h --consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h -+peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) -+consensus.o: consensus.c $(htslib_hts_h) rbuf.h $(bcftools_h) - version.o: version.h version.c - - test/test-rbuf.o: test/test-rbuf.c rbuf.h -@@ -180,8 +170,8 @@ +@@ -180,8 +172,8 @@ test/test-rbuf: test/test-rbuf.o $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) @@ -122,3 +67,5 @@ doc/bcftools.1: doc/bcftools.txt cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt +Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.orig +Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.rej |