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CFLAGS += -Wall -fopenmp
CC = g++ -O2 $(CFLAGS)
TARGETS = perm
LIBS = -lm -lstdc++ -lbsd
PER_M = AlignmentsQ.cpp Filename.cpp GenomeNTdata.cpp ReadInBits.cpp PerM.cpp chromosomeNTdata.cpp\
bitsOperationUtil.cpp FileOutputBuffer.cpp HashIndexT.cpp ReadInBitsSet.cpp SeedPattern.cpp\
boolFlagArray.cpp GenomeInBits.cpp Index_Table.cpp ReadsMapping.cpp PairedReadsMapping.cpp ShortReadUtil.cpp\
chdir.cpp Genome_Index.cpp MismatchScores.cpp stdafx.cpp Flags.cpp ParseReadsOpts.cpp\
ColorSpaceRead.cpp Genome_Index_Table.cpp ParameterList.cpp ReadsMappingStats.cpp\
FileInputBuffer.cpp Genome_Index_TableQ.cpp ReadsQualScores.cpp ChrIndex2GeneName.cpp\
ReadsFileParser.cpp PairedReadsSet.cpp MappingResult.cpp refInBinFile.cpp LongReadsSet.cpp
all: $(TARGETS)
# -ctags *.[ch]
install: all
strip $(TARGETS)
cp $(TARGETS) /usr/local/sbin
cp *.1 /usr/local/man/man1
perm: $(PER_M)
make clean
$(CC) -o $@ $(CFLAGS) $(LIB_PATH) $(PER_M) $(LIBS) $(LDFLAGS) $(CPPFLAGS)
#$(CC) -o $@ $(LIB_PATH) *.o $(LIBS)
tar: clean
tar cvfz $(TARGETS).tar.gz *.cpp *.h makefile
clean:
-rm -f *.o *.exe cut out $(TARGETS) $(TARGETS).tar.gz
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