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--- a/Makefile 2017-03-13 09:55:48.000000000 -0500
+++ b/Makefile 2020-01-13 17:42:49.359554802 -0600
@@ -30,13 +30,14 @@
# Adjust $(HTSDIR) to point to your top-level htslib directory
HTSDIR = htslib-1.4
-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)
+#include $(HTSDIR)/htslib.mk
+#include $(HTSDIR)/htslib_static.mk
+HTSINC = $(HTSDIR)/include
+HTSLIB = -L$(HTSDIR)/lib -lhts
+BGZIP = $(HTSDIR)/bin/bgzip
+TABIX = $(HTSDIR)/bin/tabix
+#HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+#HTSLIB_LIBS = $(HTSLIB_static_LIBS)
CC = gcc
CPPFLAGS =
@@ -51,7 +52,7 @@
endif
# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ALL_CPPFLAGS = -I. -I$(HTSINC)
ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS)
ALL_LIBS = -lm -lz -ldl $(LIBS)
@@ -64,7 +65,7 @@
mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\"
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
@@ -73,7 +74,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
prefix = /usr/local
@@ -208,10 +209,10 @@
test/test-regidx.o: test/test-regidx.c regidx.h
-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
+test/test-regidx: test/test-regidx.o regidx.o
$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
-bcftools: $(HTSLIB) $(OBJS)
+bcftools: $(OBJS)
$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
doc/bcftools.1: doc/bcftools.txt
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