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--- src/Makefile.orig 2018-03-23 14:01:01 UTC
+++ src/Makefile
@@ -5,8 +5,9 @@
################################################################################
# Compiler
-CXX=g++ ${CXXFLAGS}
-C=gcc
+CXX ?= g++
+# CXX += ${CXXFLAGS}
+CC ?= gcc
export CXXFLAGS
export C
@@ -17,7 +18,7 @@ export LIBFLAGS
# Compiler flags
-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+CFLAGS += -D_FILE_OFFSET_BITS=64
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
SEQLIB_ROOT=../SeqLib
@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib
TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
-LIBS = -lz -llzma -lbz2 -lm -lpthread
+LIBS = -lz -llzma -lbz2 -lm -lpthread -lexecinfo
INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT)
#INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
@@ -46,10 +47,10 @@ gprof:
.PHONY: all static debug profiling gprof
$(HTSLIB_ROOT)/libhts.a:
- cd $(HTSLIB_ROOT) && make
+ cd $(HTSLIB_ROOT) && ${MAKE}
$(SEQLIB_ROOT)/src/libseqlib.a:
- cd $(SEQLIB_ROOT) && ./configure && make
+ cd $(SEQLIB_ROOT) && ./configure && ${MAKE}
OBJECTS=BedReader.o \
CNV.o \
@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $(
$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
fastlz.o: fastlz.c fastlz.h
- $(C) $(CFLAGS) $(INCLUDE) -c fastlz.c
+ $(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c
Parameters.o: Parameters.cpp Parameters.h Version.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
@@ -277,5 +278,5 @@ autoversion:
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
- if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
- make -C $(VCFLIB_ROOT)/smithwaterman clean
+ if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi
+ ${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean
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