f3fd89193f28ab85e5c51c52f20b7c8400c26350
larrym
  Tue Jan 10 15:38:06 2012 -0800
move chrom name normalizing code out of bamFile (we weren't handling stuff like 'IV' and '2L')
diff --git src/inc/bamFile.h src/inc/bamFile.h
index 8ecc78c..4563773 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -127,21 +127,22 @@
 bam1_t *bamClone(const bam1_t *bam);
 /* Return a newly allocated copy of bam. */
 
 void bamShowTags(const bam1_t *bam);
 /* Print out tags in HTML: bold key, no type indicator for brevity. */
 
 char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize);
 /* If bam's tags include the given 2-character tag, place the value into 
  * buf (zero-terminated, trunc'd if nec) and return a pointer to buf,
  * or NULL if tag is not present. */
 
 void bamUnpackAux(const bam1_t *bam, struct dyString *dy);
 /* Unpack the tag:type:val part of bam into dy */
 
 struct bamChromInfo *bamChromList(samfile_t *fh);
-/* Return list of chromosomes from bam header. We normalize chromosome names to UCSC format. */
+/* Return list of chromosomes from bam header. We make no attempty to normalize chromosome names to UCSC format,
+   so list may contain things like "1" for "chr1", "I" for "chrI", "MT" for "chrM" etc. */
 
 void bamChromInfoFreeList(struct bamChromInfo **pList);
 /* Free a list of dynamically allocated bamChromInfo's */
 
 #endif//ndef BAMFILE_H