d86dc87199b35d264f963e032a75bfdf96db8c81
angie
  Tue Feb 15 10:47:40 2011 -0800
Tweaked comment describing bamFileNameFromTable().
diff --git src/hg/inc/bamFile.h src/hg/inc/bamFile.h
index e80e231..b9e2331 100644
--- src/hg/inc/bamFile.h
+++ src/hg/inc/bamFile.h
@@ -28,32 +28,32 @@
 
 #ifndef SAMALIGNMENT_H
 #include "samAlignment.h"
 #endif
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif 
 
 char *bamFileNameFromTable(struct sqlConnection *conn, char *table, char *bamSeqName);
 /* Return file name from table.  If table has a seqName column, then grab the 
- * row associated with bamSeqName (which is not nec. in chromInfo, e.g. 
- * bam file might have '1' not 'chr1'). */
+ * row associated with bamSeqName (which can be e.g. '1' not 'chr1' if that is the
+ * case in the bam file). */
 
 boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
 void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
 	samfile_t **pSamFile);
 /* Open the .bam file, fetch items in the seq:start-end position range,
  * and call callbackFunc on each bam item retrieved from the file plus callbackData.
  * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  */
 
 struct samAlignment *bamFetchSamAlignment(char *fileOrUrl, char *chrom, int start, int end,
 	struct lm *lm);
 /* Fetch region as a list of samAlignments - which is more or less an unpacked