# This Makefile will build and generate executable for programs used by the InteMAP pipeline.



.PHONY : all
all: ctgvalidate extract_fastqread fastatrans fastqtofasta FilterCtgCov mergeassembly mergefastq-p rfheader SCFtoCTG


ctgvalidate: src/ctgvalidate/ctgvalidate.o
	g++ src/ctgvalidate/ctgvalidate.o -O3 -o ctgvalidate

src/ctgvalidate/ctgvalidate.o: src/ctgvalidate/ctgvalidate.cpp
	g++ -c src/ctgvalidate/ctgvalidate.cpp -O3 -o src/ctgvalidate/ctgvalidate.o

extract_fastqread: src/extract_fastqread/extract_fastqread.o
	g++ src/extract_fastqread/extract_fastqread.o -O3 -o extract_fastqread

src/extract_fastqread/extract_fastqread.o: src/extract_fastqread/extract_fastqread.cpp
	g++ -c src/extract_fastqread/extract_fastqread.cpp -o src/extract_fastqread/extract_fastqread.o

fastatrans: src/fastatrans/fastatrans.o
	g++ src/fastatrans/fastatrans.o -O3 -o fastatrans

src/fastatrans/fastatrans.o: src/fastatrans/fastatrans.cpp
	g++ -c src/fastatrans/fastatrans.cpp -O3 -o src/fastatrans/fastatrans.o
	
fastqtofasta: src/fastqtofasta/fastqtofasta.o
	g++ src/fastqtofasta/fastqtofasta.o -O3 -o fastqtofasta

src/fastqtofasta/fastqtofasta.o: src/fastqtofasta/fastqtofasta.cpp
	g++ -c src/fastqtofasta/fastqtofasta.cpp -O3 -o src/fastqtofasta/fastqtofasta.o

FilterCtgCov: src/FilterCtgCov/FilterCtgCov.o
	g++ src/FilterCtgCov/FilterCtgCov.o -O3 -o FilterCtgCov

src/FilterCtgCov/FilterCtgCov.o: src/FilterCtgCov/FilterCtgCov.cpp
	g++ -c src/FilterCtgCov/FilterCtgCov.cpp -O3 -o src/FilterCtgCov/FilterCtgCov.o

mergefastq-p: src/mergefastq-p/mergefastq-p.o
	g++ src/mergefastq-p/mergefastq-p.o -O3 -o mergefastq-p 

src/mergefastq-p/mergefastq-p.o: src/mergefastq-p/mergefastq-p.cpp
	g++ -c src/mergefastq-p/mergefastq-p.cpp -O3 -o src/mergefastq-p/mergefastq-p.o

rfheader: src/rfheader/rfheader.o
	g++ src/rfheader/rfheader.o -O3 -o rfheader

src/rfheader/rfheader.o: src/rfheader/refineheader.cpp
	g++ -c src/rfheader/refineheader.cpp -O3 -o src/rfheader/rfheader.o

SCFtoCTG: src/SCFtoCTG/SCFtoCTG.o
	g++ src/SCFtoCTG/SCFtoCTG.o -O3 -o SCFtoCTG

src/SCFtoCTG/SCFtoCTG.o: src/SCFtoCTG/SCFtoCTG.cpp
	g++ -c src/SCFtoCTG/SCFtoCTG.cpp -O3 -o src/SCFtoCTG/SCFtoCTG.o
	

	
	
	