All MultiVariantWalkers should --ignore-variants-starting-outside-interval

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsWrapper.java

@@ -41,6 +41,7 @@ public void execute(File referenceFasta, File outputFile, @Nullable List<String>
             args.add(gvcf.getPath());
         }
 
+        args.add("--ignore-variants-starting-outside-interval");
         args.add("-O");
         args.add(outputFile.getPath());
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/MergeVcfsAndGenotypesWrapper.java

@@ -47,6 +47,7 @@ public void execute(File referenceFasta, List<File> inputVcfs, File outputVcf, L
         args.add("MergeVcfsAndGenotypes");
         args.add("-R");
         args.add(referenceFasta.getPath());
+        args.add("--ignore-variants-starting-outside-interval");
 
         List<String> priorities = new ArrayList<>();
         int idx = 0;

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

@@ -35,6 +35,7 @@ public File execute(File inputVCF, File referenceFasta, File outputHtml, List<St
         args.add(inputVCF.getPath());
         args.add("-O");
         args.add(outputHtml.getPath());
+        args.add("--ignore-variants-starting-outside-interval");
         if (options != null)
         {
             args.addAll(options);

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

@@ -114,6 +114,8 @@ public void runTool(File inputVCF, File refVcf, File outputTable, File outputTab
             args.add("-O");
             args.add(outputTable.getPath());
 
+            args.add("--ignore-variants-starting-outside-interval");
+
             args.add("-sites-output");
             args.add(outputTableSites.getPath());