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Makefile
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Makefile
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PROGRAM_NAME = sickle
VERSION = 1.33
CXX = g++
CXXFLAGS = -std=c++17 -Wall -DVERSION=$(VERSION)
DEBUG = -g
OPT = -O3
ARCHIVE = $(PROGRAM_NAME)_$(VERSION)
LDFLAGS=
LIBS = -lz -lpthread -lstdc++fs
SDIR = src
.PHONY: clean default build distclean dist debug
default: build
trim.o: $(SDIR)/trim.cpp $(SDIR)/trim.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
trim_single.o: $(SDIR)/trim_single.cpp $(SDIR)/trim_single.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
trim_paired.o: $(SDIR)/trim_paired.cpp $(SDIR)/trim_paired.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
sickle.o: $(SDIR)/sickle.cpp $(SDIR)/sickle.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
GZReader.o: $(SDIR)/GZReader.cpp $(SDIR)/GZReader.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
FQEntry.o: $(SDIR)/FQEntry.cpp $(SDIR)/FQEntry.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
Batch.o: $(SDIR)/Batch.cpp $(SDIR)/Batch.h
$(CXX) $(CXXFLAGS) $(OPT) -c $(SDIR)/$*.cpp
clean:
rm -rf *.o $(SDIR)/*.gch ./sickle
distclean: clean
rm -rf *.tar.gz
dist:
tar -zcf $(ARCHIVE).tar.gz src Makefile README.md sickle.xml LICENSE
build: Batch.o GZReader.o FQEntry.o trim.o trim_single.o trim_paired.o sickle.o
$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OPT) $? -o sickle $(LIBS)
debug:
$(MAKE) build "CXXFLAGS=-Wall -pedantic -D__STDC_LIMIT_MACROS -g -DDEBUG"
test_pe:
./sickle pe -f test/test.f.fastq -r test/test.r.fastq -t sanger\
-o test/output/test_pe1.trim.fastq -p test/output/test_pe2.trim.fastq -s test/output/test_s.trim.fastq\
-q 60 > test/output/test_pe.trim.txt
test_pei:
./sickle pe -c test/test.fastq -t sanger -M test/output/test_pei.trim.fastq -q 60 > test/output/test_pei.trim.txt
test_se:
./sickle se -f test/test.fastq -t sanger -o test/output/test.trim.fastq -q 60 > test/output/test.trim.txt