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--- Makefile.orig 2017-03-14 07:26:49.191430557 +0100
+++ Makefile 2017-03-14 07:27:44.929678345 +0100
@@ -29,20 +29,10 @@
all: $(PROG) $(TEST_PROG)
# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = htslib-1.4.1
-include $(HTSDIR)/htslib.mk
-include $(HTSDIR)/htslib_static.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP = $(HTSDIR)/bgzip
-TABIX = $(HTSDIR)/tabix
-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-HTSLIB_LIBS = $(HTSLIB_static_LIBS)
+HTSDIR = /usr/include
CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
-LDFLAGS =
-LIBS =
+CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS)
ifeq "$(shell uname -s)" "Darwin"
DYNAMIC_FLAGS = -Wl,-export_dynamic
@@ -51,8 +41,8 @@
endif
# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
-ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS)
+ALL_CPPFLAGS = -I. $(CPPFLAGS)
+ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(LDFLAGS)
ALL_LIBS = -lm -lz -ldl $(LIBS)
OBJS = main.o vcfindex.o tabix.o \
@@ -64,7 +54,7 @@
mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\"
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
@@ -73,7 +63,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
prefix = /usr/local
@@ -117,12 +107,12 @@
.c.o:
$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
-test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX)
+test: $(PROG) plugins test/test-rbuf test/test-regidx
./test/test-regidx
- ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+ ./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
@@ -208,11 +198,11 @@
test/test-regidx.o: test/test-regidx.c regidx.h
-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
- $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
+test/test-regidx: test/test-regidx.o regidx.o
+ $(CC) $(ALL_LDFLAGS) -o $@ $^ -lpthread -lhts $(ALL_LIBS)
-bcftools: $(HTSLIB) $(OBJS)
- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
+bcftools: $(OBJS)
+ $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread -lhts $(GSL_LIBS) $(ALL_LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
|