Merge pull request #1099 from GMOD/fix_initial_fetch_bam

Fix initial fetch bam

release-notes.md

@@ -3,9 +3,10 @@
 ## Minor improvements
 
  * Added support for the CSI index format for VCF and BAM files! This format enables genomes
-   with chromosomes longer than a gigabase to be used in JBrowse. To enable, use the
-   `csiUrlTemplate` config to point to the file. Thanks to Keiran Raine and others for
-   motivating this! (issue #926, pull #1086, @cmdcolin)
+   with individual chromosomes longer than ~537MB (2^29 bases) to be used in JBrowse. To enable,
+   use the `csiUrlTemplate` config to point to the file. Thanks to Keiran Raine for initial
+   report and Nathan S Watson-Haigh for catching a bug in the initial implementation!
+   (issue #926, pull #1086, @cmdcolin)
 
  * Added a `dontRedispatch` option for GFF3Tabix stores. Example: set `dontRedispatch=region`
    if there are `region` biotype features in the GFF that do not have subfeatures which will

src/JBrowse/Model/CSIIndex.js

@@ -105,6 +105,8 @@ return declare( TabixIndex, {
             // the linear index
 
         }
+
+        this.minAlignmentVO = this.firstDataLine;
         deferred.resolve({ success: true });
     },
 

src/JBrowse/Store/SeqFeature/BAM/File.js

@@ -86,7 +86,7 @@ var BamFile = declare( null,
         // BGZF block, assuming BGZF blocks are no bigger than 64KB.
         thisB.data.read(
             0,
-            thisB.minAlignmentVO ? thisB.minAlignmentVO.block + 65535 : null,
+            thisB.index.minAlignmentVO ? thisB.index.minAlignmentVO.block + 65535 : null,
             function(r) {
                 try {
                     var uncba;