Use BGZF* in cram_index_build() instead of zfp*

Makefile

@@ -176,8 +176,7 @@ LIBHTS_OBJS = \
 	cram/rANS_static.o \
 	cram/sam_header.o \
 	cram/string_alloc.o \
-	cram/vlen.o \
-	cram/zfio.o
+	cram/vlen.o
 
 PLUGIN_EXT  =
 PLUGIN_OBJS =
@@ -320,7 +319,7 @@ cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
 cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_endian_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
-cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h) cram/zfio.h
+cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
 cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
 cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
@@ -333,7 +332,6 @@ cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_he
 cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
 thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h)
 cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h $(cram_os_h)
-cram/zfio.o cram/zfio.pico: cram/zfio.c config.h $(cram_os_h) cram/zfio.h
 
 
 bgzip: bgzip.o libhts.a

cram/cram_index.c

@@ -60,11 +60,11 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <sys/stat.h>
 #include <math.h>
 
+#include "htslib/bgzf.h"
 #include "htslib/hfile.h"
 #include "hts_internal.h"
 #include "cram/cram.h"
 #include "cram/os.h"
-#include "cram/zfio.h"
 
 #if 0
 static void dump_index_(cram_index *e, int level) {
@@ -450,12 +450,13 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r) {
  * decode the slice to look at the RI data series instead.
  *
  * Returns 0 on success
- *        -1 on failure
+ *        -1 on read failure
+ *        -4 on write failure
  */
 static int cram_index_build_multiref(cram_fd *fd,
 				     cram_container *c,
 				     cram_slice *s,
-				     zfp *fp,
+				     BGZF *fp,
 				     off_t cpos,
 				     int32_t landmark,
 				     int sz) {
@@ -477,7 +478,8 @@ static int cram_index_build_multiref(cram_fd *fd,
 	    sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
 		    ref, ref_start, ref_end - ref_start + 1,
 		    (int64_t)cpos, landmark, sz);
-	    zfputs(buf, fp);
+	    if (bgzf_write(fp, buf, strlen(buf)) < 0)
+		return -4;
 	}
 
 	ref = s->crecs[i].ref_id;
@@ -489,7 +491,8 @@ static int cram_index_build_multiref(cram_fd *fd,
 	sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
 		ref, ref_start, ref_end - ref_start + 1,
 		(int64_t)cpos, landmark, sz);
-	zfputs(buf, fp);
+	if (bgzf_write(fp, buf, strlen(buf)) < 0)
+	    return -4;
     }
 
     return 0;
@@ -509,7 +512,7 @@ static int cram_index_build_multiref(cram_fd *fd,
 int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
     cram_container *c;
     off_t cpos, spos, hpos;
-    zfp *fp;
+    BGZF *fp;
     kstring_t fn_idx_str = {0};
 
     if (! fn_idx) {
@@ -518,7 +521,7 @@ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
         fn_idx = fn_idx_str.s;
     }
 
-    if (!(fp = zfopen(fn_idx, "wz"))) {
+    if (!(fp = bgzf_open(fn_idx, "wg"))) {
         perror(fn_idx);
         free(fn_idx_str.s);
         return -4;
@@ -549,30 +552,35 @@ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
         for (j = 0; j < c->num_landmarks; j++) {
             char buf[1024];
             cram_slice *s;
-            int sz;
+            int sz, ret;
 
             spos = htell(fd->fp);
             assert(spos - cpos - c->offset == c->landmark[j]);
 
             if (!(s = cram_read_slice(fd))) {
-		zfclose(fp);
+		bgzf_close(fp);
 		return -1;
 	    }
 
             sz = (int)(htell(fd->fp) - spos);
 
 	    if (s->hdr->ref_seq_id == -2) {
-		cram_index_build_multiref(fd, c, s, fp,
-					  cpos, c->landmark[j], sz);
+		ret = cram_index_build_multiref(fd, c, s, fp,
+						cpos, c->landmark[j], sz);
 	    } else {
 		sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
 			s->hdr->ref_seq_id, s->hdr->ref_seq_start,
 			s->hdr->ref_seq_span, (int64_t)cpos,
 			c->landmark[j], sz);
-		zfputs(buf, fp);
+		ret = (bgzf_write(fp, buf, strlen(buf)) >= 0)? 0 : -4;
 	    }
 
             cram_free_slice(s);
+
+	    if (ret < 0) {
+		bgzf_close(fp);
+		return ret;
+	    }
         }
 
         cpos = htell(fd->fp);
@@ -581,10 +589,9 @@ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
         cram_free_container(c);
     }
     if (fd->err) {
-	zfclose(fp);
+	bgzf_close(fp);
 	return -1;
     }
-
 
-    return (zfclose(fp) >= 0)? 0 : -4;
+    return (bgzf_close(fp) >= 0)? 0 : -4;
 }

htslib.mk

@@ -141,9 +141,7 @@ HTSLIB_ALL = \
 	$(HTSDIR)/cram/string_alloc.c \
 	$(HTSDIR)/cram/string_alloc.h \
 	$(HTSDIR)/cram/vlen.c \
-	$(HTSDIR)/cram/vlen.h \
-	$(HTSDIR)/cram/zfio.c \
-	$(HTSDIR)/cram/zfio.h
+	$(HTSDIR)/cram/vlen.h
 
 $(HTSDIR)/config.h:
 	+cd $(HTSDIR) && $(MAKE) config.h