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Author: Steffen Möller
Last-Update: 2019-03-16 16:13:25 +0100
Description: Use Debian packaged libs
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,8 @@
#-- for now these MUST point to the included "samtools-0.x.x" and "gclib" sub-directories
-BAM := ./samtools-0.1.18
GDIR := ./gclib
#--
-INCDIRS := -I. -I${GDIR} -I${BAM}
+INCDIRS := -I. -I${GDIR} -I/usr/include/samtools -I/usr/include/htslib
CXX := $(if $(CXX),$(CXX),g++)
@@ -24,9 +23,7 @@
LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
-LDFLAGS += -L${BAM}
-
-LIBS := -lbam -lz
+LIBS := -lhts -lbam -lz
ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
NOTHREADS=1
@@ -150,9 +147,7 @@
rlink.o : rlink.h tablemaker.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h
tmerge.o : rlink.h tmerge.h
tablemaker.o : tablemaker.h rlink.h
-${BAM}/libbam.a:
- cd ${BAM} && make lib
-stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
+stringtie: $(OBJS) stringtie.o
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
@echo
${DBG_WARN}
@@ -167,6 +162,5 @@
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
allclean cleanAll cleanall:
- cd ${BAM} && make clean
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
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