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HTS_DIR = ../
include $(HTS_DIR)/htslib_static.mk
CC = gcc
CFLAGS = -Wall -O2
#to statically link to libhts
LDFLAGS = $(HTS_DIR)/libhts.a -L$(HTS_DIR) $(HTSLIB_static_LDFLAGS) $(HTSLIB_static_LIBS)
#to dynamically link to libhts
#LDFLAGS = -L $(HTS_DIR) -lhts -Wl,-rpath,<installed lib path>
PRGS = flags split split2 cram read_fast read_header read_ref read_bam \
read_aux dump_aux add_header rem_header update_header mod_bam mod_aux \
mod_aux_ba write_fast idx_on_write read_reg read_multireg pileup \
mpileup modstate pileup_mod flags_field split_t1 split_t2 \
read_fast_i qtask_ordered qtask_unordered index_fasta
all: $(PRGS)
flags: flags_demo.c
$(CC) $(CFLAGS) -I $(HTS_DIR) flags_demo.c -o $@ $(LDFLAGS)
split: split.c
$(CC) $(CFLAGS) -I $(HTS_DIR) split.c -o $@ $(LDFLAGS)
split2: split2.c
$(CC) $(CFLAGS) -I $(HTS_DIR) split2.c -o $@ $(LDFLAGS)
cram: cram.c
$(CC) $(CFLAGS) -I $(HTS_DIR) cram.c -o $@ $(LDFLAGS)
read_fast: read_fast.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_fast.c -o $@ $(LDFLAGS)
read_header: read_header.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_header.c -o $@ $(LDFLAGS)
read_ref: read_refname.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_refname.c -o $@ $(LDFLAGS)
read_bam: read_bam.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_bam.c -o $@ $(LDFLAGS)
read_aux: read_aux.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_aux.c -o $@ $(LDFLAGS)
dump_aux: dump_aux.c
$(CC) $(CFLAGS) -I $(HTS_DIR) dump_aux.c -o $@ $(LDFLAGS)
add_header: add_header.c
$(CC) $(CFLAGS) -I $(HTS_DIR) add_header.c -o $@ $(LDFLAGS)
rem_header: rem_header.c
$(CC) $(CFLAGS) -I $(HTS_DIR) rem_header.c -o $@ $(LDFLAGS)
update_header: update_header.c
$(CC) $(CFLAGS) -I $(HTS_DIR) update_header.c -o $@ $(LDFLAGS)
mod_bam: mod_bam.c
$(CC) $(CFLAGS) -I $(HTS_DIR) mod_bam.c -o $@ $(LDFLAGS)
mod_aux: mod_aux.c
$(CC) $(CFLAGS) -I $(HTS_DIR) mod_aux.c -o $@ $(LDFLAGS)
mod_aux_ba: mod_aux_ba.c
$(CC) $(CFLAGS) -I $(HTS_DIR) mod_aux_ba.c -o $@ $(LDFLAGS)
write_fast: write_fast.c
$(CC) $(CFLAGS) -I $(HTS_DIR) write_fast.c -o $@ $(LDFLAGS)
idx_on_write: index_write.c
$(CC) $(CFLAGS) -I $(HTS_DIR) index_write.c -o $@ $(LDFLAGS)
read_reg: index_reg_read.c
$(CC) $(CFLAGS) -I $(HTS_DIR) index_reg_read.c -o $@ $(LDFLAGS)
read_multireg: index_multireg_read.c
$(CC) $(CFLAGS) -I $(HTS_DIR) index_multireg_read.c -o $@ $(LDFLAGS)
read_fast_i: read_fast_index.c
$(CC) $(CFLAGS) -I $(HTS_DIR) read_fast_index.c -o $@ $(LDFLAGS)
pileup: pileup.c
$(CC) $(CFLAGS) -I $(HTS_DIR) pileup.c -o $@ $(LDFLAGS)
mpileup: mpileup.c
$(CC) $(CFLAGS) -I $(HTS_DIR) mpileup.c -o $@ $(LDFLAGS)
modstate: modstate.c
$(CC) $(CFLAGS) -I $(HTS_DIR) modstate.c -o $@ $(LDFLAGS)
pileup_mod: pileup_mod.c
$(CC) $(CFLAGS) -I $(HTS_DIR) pileup_mod.c -o $@ $(LDFLAGS)
flags_field: flags_htsopt_field.c
$(CC) $(CFLAGS) -I $(HTS_DIR) flags_htsopt_field.c -o $@ $(LDFLAGS)
split_t1: split_thread1.c
$(CC) $(CFLAGS) -I $(HTS_DIR) split_thread1.c -o $@ $(LDFLAGS)
split_t2: split_thread2.c
$(CC) $(CFLAGS) -I $(HTS_DIR) split_thread2.c -o $@ $(LDFLAGS)
index_fasta: index_fasta.c
$(CC) $(CFLAGS) -I $(HTS_DIR) index_fasta.c -o $@ $(LDFLAGS)
qtask_ordered: qtask_ordered.c
$(CC) $(CFLAGS) -I $(HTS_DIR) qtask_ordered.c -o $@ $(LDFLAGS)
qtask_unordered: qtask_unordered.c
$(CC) $(CFLAGS) -I $(HTS_DIR) qtask_unordered.c -o $@ $(LDFLAGS)
clean:
find . -name "*.o" | xargs rm -rf
find . -name "*.dSYM" | xargs rm -rf
-rm -f $(PRGS)
|
