fdb4b5d215ff23b0f066a9b7d7a96ae31045a347
braney
  Fri Jan 15 12:27:29 2016 -0800
yet more work on support CRAM under htslib

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 1bded69..4c27828 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -75,30 +75,40 @@
  * 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. */
 
 #ifdef USE_HTS
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header,  bam_index_t *idx, char *bamFileName, 
 #else
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_index_t *idx, char *bamFileName, 
 #endif
 			 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 bamFetchPlus(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
+		 samfile_t **pSamFile, char *refUrl, char *cacheDir);
+/* 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.  
+ * refUrl points to the place to grab CRAM reference sequences (if any)
+ * cacheDir points to the directory in which CRAM reference sequences are cached */
+
 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.  */
 
 void bamClose(samfile_t **pSamFile);
 /* Close down a samefile_t */
 
 boolean bamIsRc(const bam1_t *bam);
 /* Return TRUE if alignment is on - strand. */
 
 INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)