Small changes to reference fetching logic

Author: ThomasHickman

Makefile

@@ -175,7 +175,6 @@ cram_os_h = cram/os.h $(htslib_hts_endian_h)
 cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
 cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
 cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h $(htslib_khash_h)
-cram_op]en_trace_file_h = cram/open_trace_file.h cram/mFILE.h
 
 hfile_internal_h = hfile_internal.h $(htslib_hfile_h) $(textutils_internal_h)
 hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)

cram/cram_io.c

@@ -1924,8 +1924,9 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
     int no_m5 = 0;
     char* ref_fn;
 
-    if (!(tag = sam_hdr_find_key(fd->header, ty, "M5", NULL)))
+    if (!(tag = sam_hdr_find_key(fd->header, ty, "M5", NULL))){
         no_m5 = 1;
+    }
     else {
         const char* m5_str = tag->str+3;
         hts_log_info("Querying ref %s", m5_str);

htslib/ref.h

@@ -35,7 +35,7 @@ extern "C" {
 
 /* m5_to_ref() - returns the reference genome that has a given MD5 string
  * @param m5_str: The m5 string to query
- * @returns: A hFile with a reference genome
+ * @returns: A hFILE containing a file pointer to a reference genome.
  *           NULL on failure
  *
  * Note: This function is not currently thread safe, so locks
@@ -47,7 +47,7 @@ hFILE* m5_to_ref(const char *m5_str);
 /* m5_to_path() - returns a path to a reference genome that has a
  * given MD5 string
  * @param m5_str: The m5 string to query
- * @returns: A path to a reference genome
+ * @returns: A path to the correct reference genome.
  *           NULL on failure
  *
  * Note: This function is not currently thread safe, so locks