CXX = g

CXXFLAGS= -O3 -g #-pg #-Wall #-O3

LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19 -I./htslib-1.15.1/ -L./htslib-1.15.1/

LINKFLAGS = -lpthread -lz

DEBUG=

OBJECTS =

# Change to 1 if need to parse CRAM file

htslib=0

BAMFLAGS =

ifeq ($(htslib),1)

CXXFLAGS = -DHTSLIB

BAMFLAGS = -lhts

else

BAMFLAGS = -lbam

endif

#asan=1

ifneq ($(asan),)

CXXFLAGS =-fsanitize=address

LDFLAGS =-fsanitize=address -ldl

endif

all: fastq-extractor bam-extractor genotyper analyzer

genotyper: Genotyper.o

$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)

analyzer: Analyzer.o

$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)

bam-extractor: BamExtractor.o

if [ $(htslib) -eq 1 ] ; then \

if [ ! -f ./htslib-1.15.1/libhts.a ] ; \

then \

cd htslib-1.15.1 ; \

cd htscodecs ; autoreconf -i ; ./configure ; make ; \

cd .. \

autoreconf -i ; ./configure ; make ; \

fi \

else \

if [ ! -f ./samtools-0.1.19/libbam.a ] ; \

then \

cd samtools-0.1.19 ; make ;\

fi \

fi ;

$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS) $(BAMFLAGS)

fastq-extractor: FastqExtractor.o

$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)

Genotyper.o: Genotyper.cpp Genotyper.hpp AlignAlgo.hpp ReadFiles.hpp kseq.h SeqSet.hpp KmerIndex.hpp SimpleVector.hpp defs.h KmerCode.hpp KmerCount.hpp

Analyzer.o: Analyzer.cpp Genotyper.hpp AlignAlgo.hpp ReadFiles.hpp kseq.h SeqSet.hpp KmerIndex.hpp SimpleVector.hpp defs.h KmerCode.hpp KmerCount.hpp VariantCaller.hpp BarcodeSummary.hpp

BamExtractor.o: BamExtractor.cpp alignments.hpp defs.h SeqSet.hpp

FastqExtractor.o: FastqExtractor.cpp ReadFiles.hpp defs.h SeqSet.hpp BarcodeCorrector.hpp SimpleVector.hpp

#Alignment.o: Alignment.cpp Alignment.h SimpleVector.h defs.h StatsTests.h KmerTree.h ReadSet.h KmerIndex.h poa.h

clean:

rm -f *.o *.gch genotyper analyzer bam-extractor fastq-extractor