b8e0d71f2c84ad4a431c467094183671d5e81c3e
braney
  Wed Feb 10 10:59:21 2016 -0800
assume BAM index is in fileName.bai #16800

diff --git src/lib/bamFile.c src/lib/bamFile.c
index 3c4dbc0..ebd3408 100644
--- src/lib/bamFile.c
+++ src/lib/bamFile.c
@@ -7,31 +7,34 @@
 #include "portable.h"
 #include "bamFile.h"
 #ifdef USE_BAM
 #include "htmshell.h"
 #include "udc.h"
 
 #ifdef KNETFILE_HOOKS
 // If KNETFILE_HOOKS is used (as recommended!), then we can simply call bam_index_load
 // without worrying about the samtools lib creating local cache files in cgi-bin:
 
 #ifdef USE_HTS
 static bam_index_t *bamOpenIdx(samfile_t *sam, char *fileOrUrl)
 /* If fileOrUrl has a valid accompanying .bai file, parse and return the index;
  * otherwise return NULL. */
 {
-bam_index_t *idx = sam_index_load(sam, fileOrUrl);
+char indexName[4096];
+// assume that index is a .bai file 
+safef(indexName, sizeof indexName, "%s.bai", fileOrUrl);
+bam_index_t *idx = sam_index_load2(sam, fileOrUrl, indexName);
 return idx;
 }
 #else
 static bam_index_t *bamOpenIdx(char *fileOrUrl)
 /* If fileOrUrl has a valid accompanying .bai file, parse and return the index;
  * otherwise return NULL. */
 {
 bam_index_t *idx = bam_index_load(fileOrUrl);
 return idx;
 }
 #endif
 
 #else// no KNETFILE_HOOKS
 // Oh well.  The unmodified samtools lib downloads .bai files into the current
 // working directory, which is cgi-bin -- not good.  So we need to temporarily