118 lines
3.4 KiB
Makefile
118 lines
3.4 KiB
Makefile
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)
|