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Makefile.debug
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Makefile.debug
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PROG= PISA
all: $(PROG)
HTSDIR = third_party/htslib-1.10.2
include $(HTSDIR)/htslib.mk
HTSLIB = $(HTSDIR)/libhts.a
HTSVERSION = $(HTSDIR)/version.h
#FMLDIR = third_party/fermi-lite
#include $(FMLDIR)/fermi.mk
#FMLLIB = $(FMLDIR)/libfml.a
LIBA = src/liba.a
ZLIBDIR= third_party/zlib-1.2.11
include $(ZLIBDIR)/zlib.mk
LIBZ = $(ZLIBDIR)/libz.a
CC = gcc
CFLAGS = -Wall -O0 -g -D_FILE_OFFSET_BITS=64 -fopenmp
DFLAGS =
INCLUDES = -Isrc -I$(HTSDIR)/ -I. -I$(ZLIBDIR)
LIBS = -lbz2 -llzma -pthread -lm -lcurl
#all:$(PROG)
# See htslib/Makefile
PACKAGE_VERSION := $(shell git describe --tags)
.SUFFIXES:.c .o
.PHONY:all clean clean-all distclean install lib tags test testclean
force:
.c.o:
@printf "Compiling $<... \r"
@$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
LIB_OBJ = src/barcode_list.o \
src/bam_anno_vcf.o \
src/bed.o \
src/number.o \
src/fastq.o \
src/kson.o \
src/json_config.o \
src/gtf.o \
src/region_index.o \
src/dict.o \
src/ksa.o \
src/bam_pool.o \
src/umi_corr.o \
src/dict.o \
src/read_tags.o \
src/sim_search.o \
src/fragment.o \
src/compactDNA.o \
src/bam_region.o \
src/dna_pool.o \
src/bam_files.o \
src/biostring.o \
src/read_anno.o \
src/kthread.o \
src/coverage.o
AOBJ = src/bam_anno.o \
src/bam_count.o \
src/bam_pick.o \
src/sam2bam.o \
src/bam_attr_count.o \
src/fastq_sort.o \
src/fastq_parse_barcode.o \
src/bam_tag_corr.o \
src/bam2fq.o \
src/bam_extract_tags.o \
src/bam_rmdup.o\
src/gene_fusion.o \
src/bam_depth.o \
src/usage.o \
src/addtags.o \
src/fragment_count.o \
src/fastq_stream.o \
src/fastq_parse2.o \
src/gtf_format.o \
src/callept.o \
src/bed_merge.o \
src/bed_anno.o \
src/gtf2bed.o \
src/bed_flatten.o
liba.a: $(LIB_OBJ)
@-rm -f src/$@
$(AR) -rcs src/$@ $(LIB_OBJ)
test: $(HTSLIB) $(HTSVERSION)
PISA: $(HTSLIB) $(LIBZ) liba.a $(AOBJ)
$(CC) $(CFLAGS) $(INCLUDES) -o $@ src/main.c $(AOBJ) src/liba.a $(HTSLIB) $(LIBS) $(LIBZ)
git:
@-echo '#define PISA_VERSION "$(PACKAGE_VERSION)"' > pisa_version.h
@-git push
src/gtf_format.o: src/gtf_format.c
src/fastq_parse2.o: src/fastq_parse2.c
src/fastq_stream.o: src/fastq_stream.c
src/read_anno.o: src/read_anno.c
src/sim_search.o: src/sim_search.c
src/bam_depth.o: src/bam_depth.c
src/bam2fq.o: src/bam2fq.c
src/bam_anno.o: src/bam_anno.c
src/bam_count.o: src/bam_count.c
src/bam_pick.o: src/bam_pick.c
src/bam_anno_vcf.o: src/bam_anno_vcf.c
src/bam_tag_corr.o: src/bam_tag_corr.c
src/umi_corr.o: src/umi_corr.c
src/fastq_parse_barcode.o: src/fastq_parse_barcode.c
src/fastq_sort.o: src/fastq_sort.c
src/dict.o: src/dict.c
src/sam2bam.o: src/sam2bam.c
src/barcode_list.o: src/barcode_list.c
src/bed.o: src/bed.c
src/number.o: src/number.c
src/gtf.o: src/gtf.c
src/region_index.o: src/region_index.c
src/dict.o: src/dict.c
src/fastq.o: src/fastq.c
src/json_config.o: src/json_config.c
src/kson.o: src/kson.c
src/bam_attr_count.o: src/bam_attr_count.c
src/read_tags.o: src/read_tags.c
src/ksa.o: src/ksa.c
src/bam_pool.o: src/bam_pool.c
src/bam_extract_tags.o: src/bam_extract_tags.c
src/usage.o:src/usage.c
src/bam_rmdup.o:src/bam_rmdup.c
src/dna_pool.o:src/dna_pool.c
src/gene_fusion.o:src/gene_fusion.c
src/bam_files.o:src/bam_files.c
src/biostring.o:src/biostring.c
src/kthread.o:src/kthread.c
src/addtags.o:src/addtags.c
src/fragment.o:src/fragment_count.c
clean: testclean
-rm -f gmon.out *.o *~ $(PROG)
-rm -rf *.dSYM plugins/*.dSYM test/*.dSYM
-rm src/*.o src/liba.a
testclean:
-rm -f test/*.o test/*~ $(TEST_PROG)
distclean: clean
-rm -f TAGS
clean-all: clean clean-htslib
tags:
ctags -f TAGS src/*.[ch] $(HTSDIR)/*.c