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| author | Christian Krause | 2016-03-05 11:40:11 +0100 |
|---|---|---|
| committer | Christian Krause | 2016-03-05 11:40:11 +0100 |
| commit | 295038a40f0e6bafafc7765250919f555557a74a (patch) | |
| tree | b66c12a93ecfe2c68e1a7a422d6b1f5231ddf762 /makefile-system-htslib.patch | |
| parent | ce0e65b4a554c65329bc40d6de30120fda1aa0ea (diff) | |
| download | aur-295038a40f0e6bafafc7765250919f555557a74a.tar.gz | |
bcftools-1.3-2
Diffstat (limited to 'makefile-system-htslib.patch')
| -rw-r--r-- | makefile-system-htslib.patch | 28 |
1 files changed, 17 insertions, 11 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch index 9965be1135d7..91056165a424 100644 --- a/makefile-system-htslib.patch +++ b/makefile-system-htslib.patch @@ -1,6 +1,6 @@ ---- Makefile.orig 2016-01-10 11:15:35.126733492 +0100 -+++ Makefile 2016-01-10 11:21:31.034859116 +0100 -@@ -28,13 +28,6 @@ +--- /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 @@ all: $(PROG) $(TEST_PROG) @@ -12,9 +12,15 @@ -TABIX = $(HTSDIR)/tabix - CC = gcc - CPPFLAGS = - CFLAGS = -g -Wall -Wc++-compat -O2 -@@ -48,7 +41,7 @@ +-CPPFLAGS = +-CFLAGS = -g -Wall -Wc++-compat -O2 +-LDFLAGS = +-LIBS = ++CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS) + + 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 @@ vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling @@ -23,7 +29,7 @@ GSL_LIBS = # The polysomy command is not compiled by default because it brings dependency -@@ -57,7 +50,7 @@ +@@ -57,7 +47,7 @@ ifdef USE_GPL EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o @@ -32,7 +38,7 @@ endif prefix = /usr/local -@@ -101,11 +94,11 @@ +@@ -101,11 +91,11 @@ .c.o: $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $< @@ -48,7 +54,7 @@ # Plugin rules -@@ -136,20 +129,20 @@ +@@ -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) @@ -75,7 +81,7 @@ 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 +150,22 @@ +@@ -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) @@ -105,7 +111,7 @@ version.o: version.h version.c test/test-rbuf.o: test/test-rbuf.c rbuf.h -@@ -180,8 +173,8 @@ +@@ -180,8 +170,8 @@ test/test-rbuf: test/test-rbuf.o $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) |