26c2f650359cc1c74fb31d96109bc0f8dedbc3d7
angie
  Thu May 30 10:32:19 2019 -0700
Adding BAM and VCF item counts to hubApi's list/tracks function.  Note: older index files may not contain counts.  refs #18869, #23521

diff --git src/inc/bamFile.h src/inc/bamFile.h
index d11dc14..5da2dd1 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -38,30 +38,37 @@
 
 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. */
 
+long long bamFileItemCount(char *fileOrUrl, char *baiFileOrUrl);
+/* Return the total number of mapped items across all sequences in fileOrUrl, using index file.
+ * If baiFileOrUrl is NULL, the index file is assumed to be fileOrUrl.bai.
+ * NOTE: not all bam index files include mapped item counts, so this may return 0 even for large
+ * bam.  As of May 2019, our copy of hts_idx_get_stat does not support cram indexes
+ * (perhaps they never include counts?), so this always returns 0 for cram. */
+
 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