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--- /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)
-# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = htslib-1.3
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP = $(HTSDIR)/bgzip
-TABIX = $(HTSDIR)/tabix
-
CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
-LDFLAGS =
-LIBS =
+CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS)
OBJS = main.o vcfindex.o tabix.o \
vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
@@ -48,7 +38,7 @@
vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\"
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
@@ -57,7 +47,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
prefix = /usr/local
@@ -101,11 +91,11 @@
.c.o:
$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
-test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
- ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+test: $(PROG) plugins test/test-rbuf
+ ./test/test.pl --exec bgzip=bgzip --exec tabix=tabix
-test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
- ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+test-plugins: $(PROG) plugins test/test-rbuf
+ ./test/test.pl --plugins --exec bgzip=bgzip --exec tabix=tabix
# 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 @@
test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
-bcftools: $(HTSLIB) $(OBJS)
- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+bcftools: $(OBJS)
+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lhts -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
|