0c1d13ef4e3214c4029e098ed5ef708d15e6096f
max
  Mon Nov 21 16:34:53 2016 -0800
CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to
specify the URL of the .tbi or .bai file, in case you cannot put it
alongside the .bam or .vcf.gz file.

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 935b8e2..91883ba 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -26,55 +26,66 @@
 #define bam1_seqi bam_seqi
 #define bam_nt16_rev_table seq_nt16_str
 #define data_len l_data
 
 
 struct bamChromInfo
     {
     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);
+void bamFileAndIndexMustExist(char *fileOrUrl, char *baiFileOrUrl);
 /* 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. */
+ * takes for diagnostic info to propagate up through errCatches in calling code. 
+ * The parameter baiFileOrUrl can be NULL, defaults of <fileOrUrl>.bai. */
 
 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_hdr_t *header,  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 bamAndIndexFetchPlus(char *fileOrUrl, char *baiFileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
+		 samfile_t **pSamFile, char *refUrl, char *cacheDir);
+/* Open the .bam file with the .bai index specified by baiFileOrUrl.
+ * baiFileOrUrl can be NULL and defaults to <fileOrUrl>.bai.
+ * 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 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.