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Makefile
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Makefile
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CC = gcc
IDIR = include
ODIR = obj
SRC = src
CFLAGS = -O2 -I include -I ~/.local/include -L ~/.local/lib -L ~/.local/lib64
LIBS = -lhts -lpthread
DEPS = $(IDIR)/functions.h
OBJ = $(ODIR)/functions.o $(ODIR)/main.o
all: bin/katcher bin/list_kmers bin/add_pvalues bin/extract_qname
bin/katcher: $(OBJ)
mkdir -p bin
$(CC) $(CFLAGS) $(LIBS) -o $@ $^
bin/add_pvalues: src/add_pvalues.c src/functions.c include/functions.h
mkdir -p bin
$(CC) $(CFLAGS) $(LIBS) -o bin/add_pvalues src/add_pvalues.c src/functions.c
bin/list_kmers: src/list_kmers.c
mkdir -p bin
$(CC) $(CFLAGS) $(LIBS) src/list_kmers.c -o bin/list_kmers
bin/extract_qname: src/extract_qname.c
mkdir -p bin
$(CC) $(CFLAGS) $(LIBS) -o bin/extract_qname src/extract_qname.c
$(ODIR)/%.o: $(SRC)/%.c $(DEPS)
mkdir -p obj
$(CC) $(CFLAGS) $(LIBS) -c -o $@ $<
test: bin/katcher
bin/list_kmers test/significant_pav_table.txt SRR1533395 > test/input_kmers.txt
bin/katcher -i test/input_test.bam -k test/input_kmers.txt -o test/reads_with_kmers.bam -t6 -b 600000 -m 300
bin/add_pvalues test/reads_with_kmers.bam test/kmer_pvalues.txt > test/reads_with_pvalues.bam
bin/extract_qname test/reads_with_pvalues.bam test/input_test.bam > test/significant_pairs.bam