Support additional liftover params

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js

@@ -157,6 +157,14 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             params.dropGenotypes = this.down('#dropGenotypes').getValue();
         }
 
+        if (this.down('#useBcfTools').getValue()){
+            params.useBcfTools = this.down('#useBcfTools').getValue();
+        }
+
+        if (this.down('#doNotRetainUnmapped').getValue()){
+            params.doNotRetainUnmapped = this.down('#doNotRetainUnmapped').getValue();
+        }
+
         Ext4.Msg.wait('Saving...');
         LABKEY.Ajax.request({
             url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler', this.containerPath),

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java

@@ -176,6 +176,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
+            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", false);
 
             int chainFileId = params.getInt("chainFileId");
             File chainFile = ctx.getSequenceSupport().getCachedData(chainFileId);
@@ -214,7 +215,7 @@ else if (_vcfFileType.isType(f.getFile()))
                 }
 
                 File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + ext);
-                File unmappedOutput = new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext);
+                File unmappedOutput = doNotRetainUnmapped ? new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext) : null;
 
                 try
                 {
@@ -260,7 +261,11 @@ else if (_vcfFileType.isType(f.getFile()))
                     ctx.addSequenceOutput(so1);
                 }
 
-                if (!unmappedOutput.exists())
+                if (unmappedOutput == null)
+                {
+                    // skip
+                }
+                else if (!unmappedOutput.exists())
                 {
                     job.getLogger().info("no unmapped intervals");
                 }