update

samples/Makefile

@@ -2,7 +2,7 @@ HTS_DIR = ../
 include $(HTS_DIR)/htslib_static.mk
 
 CC = gcc
-CFLAGS = -Wall -g -O0
+CFLAGS = -Wall -O2
 
 #to statically link to libhts
 LDFLAGS = $(HTS_DIR)/libhts.a -L$(HTS_DIR) $(HTSLIB_static_LDFLAGS) $(HTSLIB_static_LIBS)
@@ -18,97 +18,97 @@ PRGS = flags split split2 cram read_fast read_header read_ref read_bam \
 
 all: $(PRGS)
 
-flags:
+flags: flags_demo.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) flags_demo.c -o $@  $(LDFLAGS)
 
-split:
+split: split.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) split.c -o $@  $(LDFLAGS)
 
-split2:
+split2: split2.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) split2.c -o $@  $(LDFLAGS)
 
-cram:
+cram: cram.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) cram.c -o $@  $(LDFLAGS)
 
-read_fast:
+read_fast: read_fast.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_fast.c -o $@  $(LDFLAGS)
 
-read_header:
+read_header: read_header.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_header.c -o $@  $(LDFLAGS)
 
-read_ref:
+read_ref: read_refname.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_refname.c -o $@  $(LDFLAGS)
 
-read_bam:
+read_bam: read_bam.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_bam.c -o $@  $(LDFLAGS)
 
-read_aux:
+read_aux: read_aux.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_aux.c -o $@  $(LDFLAGS)
 
-dump_aux:
+dump_aux: dump_aux.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) dump_aux.c -o $@  $(LDFLAGS)
 
-add_header:
+add_header: add_header.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) add_header.c -o $@  $(LDFLAGS)
 
-rem_header:
+rem_header: rem_header.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) rem_header.c -o $@  $(LDFLAGS)
 
-update_header:
+update_header: update_header.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) update_header.c -o $@  $(LDFLAGS)
 
-mod_bam:
+mod_bam: mod_bam.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) mod_bam.c -o $@  $(LDFLAGS)
 
-mod_aux:
+mod_aux: mod_aux.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) mod_aux.c -o $@  $(LDFLAGS)
 
-mod_aux_ba:
+mod_aux_ba: mod_aux_ba.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) mod_aux_ba.c -o $@  $(LDFLAGS)
 
-write_fast:
+write_fast: write_fast.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) write_fast.c -o $@  $(LDFLAGS)
 
-idx_on_write:
+idx_on_write: index_write.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) index_write.c -o $@  $(LDFLAGS)
 
-read_reg:
+read_reg: index_reg_read.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) index_reg_read.c -o $@  $(LDFLAGS)
 
-read_multireg:
+read_multireg: index_multireg_read.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) index_multireg_read.c -o $@  $(LDFLAGS)
 
-read_fast_i:
+read_fast_i: read_fast_index.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) read_fast_index.c -o $@  $(LDFLAGS)
 
-pileup:
+pileup: pileup.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) pileup.c -o $@  $(LDFLAGS)
 
-mpileup:
+mpileup: mpileup.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) mpileup.c -o $@  $(LDFLAGS)
 
-modstate:
+modstate: modstate.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) modstate.c -o $@  $(LDFLAGS)
 
-pileup_mod:
+pileup_mod: pileup_mod.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) pileup_mod.c -o $@  $(LDFLAGS)
 
-flags_field:
+flags_field: flags_htsopt_field.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) flags_htsopt_field.c -o $@  $(LDFLAGS)
 
-split_t1:
+split_t1: split_thread1.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) split_thread1.c -o $@  $(LDFLAGS)
 
-split_t2:
+split_t2: split_thread2.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) split_thread2.c -o $@  $(LDFLAGS)
 
-index_fasta:
+index_fasta: index_fasta.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) index_fasta.c -o $@  $(LDFLAGS)
 
-qtask_ordered:
+qtask_ordered: qtask_ordered.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) qtask_ordered.c -o $@  $(LDFLAGS)
 
-qtask_unordered:
+qtask_unordered: qtask_unordered.c
 	$(CC) $(CFLAGS) -I $(HTS_DIR) qtask_unordered.c -o $@  $(LDFLAGS)
 
 clean: