Update liftover default

Author: bbimber

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

@@ -120,7 +120,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             }, {
                 xtype: 'checkbox',
                 itemId: 'doNotRetainUnmapped',
-                checked: false,
+                checked: true,
                 fieldLabel: 'Do Not Retain Unmapped'
             }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)).concat([{
                 xtype: 'sequenceanalysis-variantscattergatherpanel',

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

@@ -180,7 +180,7 @@ 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);
+            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", true);
             if (!doNotRetainUnmapped && !useBcfTools)
             {
                 ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");