diff options
| -rw-r--r-- | makefile | 43 | ||||
| -rw-r--r-- | qidx.c | 20 | ||||
| -rw-r--r-- | qidx.h | 3 |
3 files changed, 57 insertions, 9 deletions
@@ -6,20 +6,24 @@ ifeq ($(BINDIR),) BINDIR := /bin endif -CMD=qidx +name := qidx +cmd := qidx + +so_major := 0 +so_minor := 1 CC=gcc -DEBUG := -fsanitize=address -O2 -CFLAGS := -Wall -pedantic -g -LDFLAGS := -lhts -lm +CFLAGS = -Wall -pedantic $(debug) +LDFLAGS := -lhts -lm -fPIC +# debug = -fsanitize=address -O2 -g SRC_EXT:=%.c _STD_BUILD=$(CC) $(CFLAGS) $(filter $(SRC_EXT) %.o, $^) -o $@ STD_BUILD=$(_STD_BUILD) $(LDFLAGS) -STD_COMPILE=$(_STD_BUILD) -c +STD_COMPILE=$(_STD_BUILD) -fPIC -c OBJS = ./util/hash.o OBJS += ./util/prime_search.o @@ -28,13 +32,36 @@ OBJS += ./util/sds/sds.o OBJS += ./util/err.o OBJS += ./qidx.o -make: $(CMD) +devname = lib$(name).so +lib_so = lib$(name).so.$(so_major).$(so_minor) +soname = lib$(name).so.$(so_major) + +make: $(cmd) $(lib_so) -$(CMD): ./main.c $(OBJS) +$(cmd): ./main.c $(OBJS) $(STD_BUILD) +$(lib_so): $(OBJS) + $(CC) $(LDFLAGS) -shared -Wl,-soname=$(soname) -fPIC -o $@ $^ + [ -n "$(soname)" ] && ln -s $(lib_so) $(soname) || true + [ -n "$(devname)" ] && ln -s $(soname) $(devname) || true + clean: - $(RM) $(CMD) $(OBJS) + $(RM) $(cmd) $(OBJS) $(devname) $(lib_so) $(soname) +.PHONY: clean %.o: %.c $(STD_COMPILE) + +.PHONY: install +install: + mkdir -p $(DESTDIR)$(PREFIX)/include $(DESTDIR)$(PREFIX)/lib + cp qidx.h $(DESTDIR)$(PREFIX)/include/qidx.h + cp -d $(lib_so) $(soname) $(devname) $(DESTDIR)$(PREFIX)/lib/ + +.PHONY: uninstall +uninstall: + rm -f $(DESTDIR)$(PREFIX)/include/qidx.h + rm -f $(DESTDIR)$(PREFIX)/lib/$(lib_so) + [ -n "$(soname)" ] && rm -f $(DESTDIR)$(PREFIX)/lib/$(soname) || true + [ -n "$(devname)" ] && rm -f $(DESTDIR)$(PREFIX)/lib/$(devname) || true @@ -670,7 +670,7 @@ qidx_err_t qidx_table_add(qidx_htable_t * tab, qidx_record_t const * rec) { return QIDX_OK; } -qidx_err_t qidx_table_get(qidx_htable_t const * tab, +static qidx_err_t qidx_table_get(qidx_htable_t const * tab, char const * qname, qidx_record_t ** rec) { qidx_bucket_t * bucket = _qidx_bucket(qname, tab); @@ -697,6 +697,24 @@ qidx_err_t qidx_table_get(qidx_htable_t const * tab, return QIDX_OK; } +qidx_err_t qidx_lookup_alnrec(qidx_fp_t * fp, + char const * qname, qidx_record_t ** rec) { + qidx_err_t err; + + if((err = qidx_table_get(fp->htab, qname, rec))) { + return err; + } + + return QIDX_OK; +} + +void qidx_free_alnrec(qidx_record_t * rec) { + free(rec->alns); + sdsfree(rec->qname); + free(rec); +} + + void qidx_record_print(FILE * file, qidx_record_t * rec) { fprintf(file, "qname: %s\n", rec->qname); for(size_t i = 0; i < rec->n_alns; i++) { @@ -54,6 +54,9 @@ typedef struct qidx_fp qidx_fp_t; qidx_err_t qidx_open(qidx_fp_t ** fp, int fd); qidx_err_t qidx_create(qidx_fp_t ** fp, int fd, uint32_t _n_buckets, uint32_t max_bucket_size); +qidx_err_t qidx_lookup_alnrec(qidx_fp_t * fp, + char const * qname, qidx_record_t ** rec); +void qidx_free_alnrec(qidx_record_t * rec); qidx_err_t qidx_close(qidx_fp_t * fp); qidx_err_t qidx_create_index3(htsFile * fp, int fd, qidx_fp_t ** q_fp, |