Fix merge conflicts

Author: bbimber

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

@@ -115,7 +115,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             },{
                 xtype: 'checkbox',
                 itemId: 'useBcfTools',
-                checked: false,
+                checked: true,
                 fieldLabel: 'Use bcftools'
             },{
                 xtype: 'checkbox',

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

@@ -101,7 +101,8 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 List<String> args = new ArrayList<>();
                 args.addAll(getClientCommandArgs(params));
 
-                wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, args);
+                boolean doReblock = params.optBoolean("doReblock", true);
+                wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, args, doReblock);
 
                 action.addOutput(outputFile, "gVCF File", false);
                 if (idxFile.exists())

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

@@ -178,6 +178,11 @@ 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);
+            if (doNotRetainUnmapped && !useBcfTools)
+            {
+                ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");
+                doNotRetainUnmapped = true;
+            }
 
             int chainFileId = params.getInt("chainFileId");
             File chainFile = ctx.getSequenceSupport().getCachedData(chainFileId);

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/HaplotypeCallerAnalysis.java

@@ -53,7 +53,10 @@ public static List<ToolParameterDescriptor> getToolDescriptors()
                 ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--dont-use-soft-clipped-bases"), "dontUseSoftClippedBases", "Don't Use Soft Clipped Bases", "If specified, we will not analyze soft clipped bases in the reads", "checkbox", null, false),
                 ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--max-alternate-alleles"), "maxAlternateAlleles", "Max Alternate Alleles", "Passed to --max-alternate-alleles", "ldk-integerfield", new JSONObject(){{
                     put("minValue", 0);
-                }}, 6)
+                }}, 6),
+                ToolParameterDescriptor.create("doReblock", "Do Reblock", "If checked, this will run Reblock GVCFs", "checkbox", new JSONObject(){{
+                    put("checked", true);
+                }}, true)
         );
     }
 
@@ -72,7 +75,8 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         List<String> args = new ArrayList<>();
         args.addAll(getClientCommandArgs());
 
-        getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), outputFile, args);
+        boolean doReblock = getProvider().getParameterByName("doReblock").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, true);
+        getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), outputFile, args, doReblock);
 
         output.addOutput(outputFile, "gVCF File");
         output.addSequenceOutput(outputFile, outputFile.getName(), "gVCF File", rs.getReadsetId(), null, referenceGenome.getGenomeId(), "GATK Version: " + getWrapper().getVersionString());

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/ImmunoGenotypingAnalysis.java

@@ -54,7 +54,7 @@
  */
 public class ImmunoGenotypingAnalysis extends AbstractCommandPipelineStep<ImmunoGenotypingWrapper> implements AnalysisStep
 {
-    public ImmunoGenotypingAnalysis(PipelineStepProvider provider, PipelineContext ctx)
+    public ImmunoGenotypingAnalysis(PipelineStepProvider<?> provider, PipelineContext ctx)
     {
         super(provider, ctx, new ImmunoGenotypingWrapper(ctx.getLogger()));
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MergeVcfsAndGenotypesHandler.java

@@ -96,11 +96,6 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             inputFiles.forEach(x -> action.addInput(x.getFile(), "Input VCF"));
 
             ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(genomeIds.iterator().next());
-            new MergeVcfsAndGenotypesWrapper(ctx.getLogger()).execute(genome.getWorkingFastaFile(), inputVCFs, outputVcf, null);
-            if (!outputVcf.exists())
-            {
-                throw new PipelineJobException("unable to find output: " + outputVcf.getPath());
-            }
 
             if (doSort)
             {
@@ -110,6 +105,16 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     SequencePipelineService.get().sortVcf(f, null, genome.getSequenceDictionary(), ctx.getLogger());
                 }
             }
+            else
+            {
+                ctx.getLogger().debug("Pre-sorting will not be performed");
+            }
+
+            new MergeVcfsAndGenotypesWrapper(ctx.getLogger()).execute(genome.getWorkingFastaFile(), inputVCFs, outputVcf, null);
+            if (!outputVcf.exists())
+            {
+                throw new PipelineJobException("unable to find output: " + outputVcf.getPath());
+            }
 
             action.addOutput(outputVcf, "Combined VCF", false);
             SequenceOutputFile so = new SequenceOutputFile();