Include deletions in LoFreq depth of coverage

Author: bbimber

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

@@ -119,7 +119,17 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         File coverageOut = new File(outputDir, SequenceAnalysisService.get().getUnzippedBaseName(outputVcf.getName()) + ".coverage");
 
         DepthOfCoverageWrapper wrapper = new DepthOfCoverageWrapper(getPipelineCtx().getLogger());
-        wrapper.run(Collections.singletonList(inputBam), coverageOut.getPath(), referenceGenome.getWorkingFastaFile(), null, true);
+        List<String> extraArgs = new ArrayList<>();
+        extraArgs.add("--includeDeletions");
+
+        //GATK4 only:
+        //extraArgs.add("--include-deletions");
+        //extraArgs.add("--omit-per-sample-statistics");
+        //extraArgs.add("--omit-interval-statistics");
+        //extraArgs.add("--min-base-quality");
+        //extraArgs.add("15");
+
+        wrapper.run(Collections.singletonList(inputBam), coverageOut.getPath(), referenceGenome.getWorkingFastaFile(), extraArgs, true);
         if (!coverageOut.exists())
         {
             throw new PipelineJobException("Unable to find file: " + coverageOut.getPath());

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

@@ -53,13 +53,18 @@ public void run(List<File> inputBams, String outputBaseName, File referenceFasta
 
         if (deleteExtraFiles)
         {
-            for (String suffix : Arrays.asList("_summary", "_statistics", "_interval_summary", "_interval_statistics", "_gene_summary", "_gene_statistics", "_cumulative_coverage_counts", "_cumulative_coverage_proportions"))
+            deleteExtraFiles(outputBaseName);
+        }
+    }
+
+    public void deleteExtraFiles(String outputBaseName)
+    {
+        for (String suffix : Arrays.asList("_summary", "_statistics", "_interval_summary", "_interval_statistics", "_gene_summary", "_gene_statistics", "_cumulative_coverage_counts", "_cumulative_coverage_proportions"))
+        {
+            File f = new File(outputBaseName + suffix);
+            if (f.exists())
             {
-                File f = new File(outputBaseName + suffix);
-                if (f.exists())
-                {
-                    f.delete();
-                }
+                f.delete();
             }
         }
     }