6d90b13178a35682a27514cf704f7b05794e7192
kent
  Wed Nov 2 14:18:48 2016 -0700
Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 499402c..935b8e2 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -157,16 +157,20 @@
 /* Unpack the tag:type:val part of bam into dy */
 
 struct bamChromInfo *bamChromList(samfile_t *fh);
 /* 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 */
 
 void samToBed(char *samIn, char *bedOut);
 /* samToBed - Convert SAM file to a pretty simple minded bed file.. */
 
 void samToOpenBed(char *samIn, FILE *f);
 /* Like samToOpenBed, but the output is the already open file f. */
 
+struct psl *bamToPslUnscored(const bam1_t *bam, const bam_hdr_t *hdr);
+/* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords,
+ * no scoring info) */
+
 #endif//ndef BAMFILE_H