Mark intermediate BAMs for deletion in pipeline

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java

@@ -708,6 +708,13 @@ private void alignSet(Readset rs, String basename, Map<ReadData, Pair<File, File
 
                     if (output.getBAM() != null)
                     {
+                        //If we have change the BAM, mark the previous for deletion
+                        if (!bam.equals(output.getBAM()))
+                        {
+                            getHelper().getFileManager().addIntermediateFile(bam);
+                            getHelper().getFileManager().addIntermediateFile(new File(bam.getPath() + ".bai"));
+                        }
+
                         bam = output.getBAM();
 
                         //can take a long time to execute

jbrowse/resources/web/jbrowse/window/ModifyJsonConfigWindow.js

@@ -63,7 +63,7 @@ Ext4.define('JBrowse.window.ModifyJsonConfigWindow', {
                         text: 'Chunk Size Limit',
                         scope: this,
                         handler: function (gridBtn) {
-                            this.addAttribute('chunkSizeLimit ', null, 'INT');
+                            this.addAttribute('chunkSizeLimit', null, 'INT');
                         }
                     },{
                         text: 'XY Plot',