f04cc66905720a6146a43fbb5aa5d9df797d32cb
kent
  Tue Apr 29 11:11:46 2014 -0700
Renaming samMustOpen to bamMustOpenLocal and putting in library.
diff --git src/inc/bamFile.h src/inc/bamFile.h
index 94aa717..84b7b45 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -35,30 +35,41 @@
     struct bamChromInfo *next;
     char *name;		/* Chromosome name */
     bits32 size;	/* Chromosome size in bases */
     };
 
 boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
 void bamFileAndIndexMustExist(char *fileOrUrl);
 /* Open both a bam file and its accompanying index or errAbort; this is what it
  * takes for diagnostic info to propagate up through errCatches in calling code. */
 
 samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
 /* Return an open bam file as well as the filename of the bam. */
 
+samfile_t *bamMustOpenLocal(char *fileName, char *mode, void *extraHeader);
+/* Open up sam or bam file or die trying.  The mode parameter is 
+ *    "r" - open SAM to read
+ *    "rb" - open BAM to read
+ *    "w" - open SAM to write
+ *    "wb" - open BAM to write
+ * The extraHeader is generally NULL in the read case, and the write case
+ * contains a pointer to a bam_header_t with information about the header.
+ * The implementation is just a wrapper around samopen from the samtools library
+ * that aborts with error message if there's a problem with the open. */
+
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_index_t *idx, char *bamFileName, 
 			 char *position, bam_fetch_f callbackFunc, void *callbackData);
 /* With the open bam file, return items the same way with the callbacks as with bamFetch() */
 /* except in this case use an already-open bam file and index (use bam_index_load and free() for */
 /* the index). It seems a little strange to pass the filename in with the open bam, but */
 /* it's just used to report errors. */
 
 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.  */