fix for incorrect failure message with invalid reference file and nul…

…l check

faidx.c

@@ -446,7 +446,7 @@ static int fai_build3_core(const char *fn, const char *fnfai, const char *fngzi)
     bgzf = bgzf_open(fn, "r");
 
     if ( !bgzf ) {
-        hts_log_error("Failed to open the file %s", fn);
+        hts_log_error("Failed to open the file %s : %s", fn, strerror(errno));
         goto fail;
     }
 

hts.c

@@ -922,6 +922,7 @@ htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
         fn = rmme;
     }
 
+    errno = 0;      //reset to ensure appropriate error display
     hfile = hopen(fn, smode);
     if (hfile == NULL) goto error;
 
@@ -938,10 +939,18 @@ htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
          fmt->format == fastq_format))
         fp->format.format = fmt->format;
 
-    if (fmt && fmt->specific)
-        if (hts_opt_apply(fp, fmt->specific) != 0)
+    if (fmt && fmt->specific) {
+        if (hts_opt_apply(fp, fmt->specific) != 0) {
+            if (((hts_opt*)fmt->specific)->opt == CRAM_OPT_REFERENCE &&
+                (errno == ENOENT || errno == EIO || errno == EBADF ||
+                  errno == EACCES || errno == EISDIR)) {
+                /* error during reference file operation
+                 for these specific errors, set the error as EINVAL */
+                errno = EINVAL;
+            }
             goto error;
-
+        }
+    }
     if ( rmme ) free(rmme);
     return fp;
 
@@ -1595,6 +1604,10 @@ htsFile *hts_hopen(hFILE *hfile, const char *fn, const char *mode)
 int hts_close(htsFile *fp)
 {
     int ret = 0, save;
+    if (!fp) {
+        errno = EINVAL;
+        return -1;
+    }
 
     switch (fp->format.format) {
     case binary_format: