Added checks to return value of hts_opt_apply.

Also made cram_set_voption set errno using a couple appropriate POSIX
error codes, to avoid confusing "Success" error messages.

Fixes #452

Author: jkbonfield

cram/cram_io.c

@@ -4399,8 +4399,10 @@ int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...) {
 int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
     refs_t *refs;
 
-    if (!fd)
+    if (!fd) {
+	errno = EBADF;
 	return -1;
+    }
 
     switch (opt) {
     case CRAM_OPT_DECODE_MD:
@@ -4480,6 +4482,7 @@ int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
 	      (major == 3 &&  minor == 0))) {
 	    fprintf(stderr, "Unknown version string; "
 		    "use 1.0, 2.0, 2.1 or 3.0\n");
+	    errno = EINVAL;
 	    return -1;
 	}
 	fd->version = major*256 + minor;
@@ -4535,6 +4538,7 @@ int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
 
     default:
 	fprintf(stderr, "Unknown CRAM option code %d\n", opt);
+	errno = EINVAL;
 	return -1;
     }
 

hts.c

@@ -400,7 +400,9 @@ htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
     if (fp == NULL) goto error;
 
     if (fmt && fmt->specific)
-        hts_opt_apply(fp, fmt->specific);
+        if (hts_opt_apply(fp, fmt->specific) != 0)
+            goto error;
+            
 
     return fp;
 
@@ -663,7 +665,11 @@ static int hts_process_opts(htsFile *fp, const char *opts) {
     if (hts_parse_opt_list(&fmt, opts) != 0)
         return -1;
 
-    hts_opt_apply(fp, fmt.specific);
+    if (hts_opt_apply(fp, fmt.specific) != 0) {
+        hts_opt_free(fmt.specific);
+        return -1;
+    }
+
     hts_opt_free(fmt.specific);
 
     return 0;