Pass -L to DepthOfCoverage in all cases

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java

@@ -1,15 +1,18 @@
 package org.labkey.api.sequenceanalysis.run;
 
+import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.math3.exception.ConvergenceException;
 import org.apache.log4j.Logger;
-import org.labkey.api.data.ConvertHelper;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
+import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
+import org.labkey.api.writer.PrintWriters;
 
 import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -103,4 +106,22 @@ protected List<String> getBaseArgs()
 
         return args;
     }
+
+    public static List<String> generateIntervalArgsForFullGenome(ReferenceGenome rg, File intervalFile) throws PipelineJobException
+    {
+        try (PrintWriter writer = PrintWriters.getPrintWriter(intervalFile))
+        {
+            SAMSequenceDictionaryExtractor.extractDictionary(rg.getSequenceDictionary().toPath()).getSequences().forEach(x -> writer.println(x.getSequenceName()));
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
+
+        List<String> ret = new ArrayList<>();
+        ret.add("-L");
+        ret.add(intervalFile.getPath());
+
+        return ret;
+    }
 }

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

@@ -142,6 +142,10 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         extraArgs.add("--omit-per-sample-statistics");
         extraArgs.add("--omit-interval-statistics");
 
+        File intervalList = new File(outputDir, "depthOfCoverageIntervals.intervals");
+        output.addIntermediateFile(intervalList);
+        extraArgs.addAll(DepthOfCoverageWrapper.generateIntervalArgsForFullGenome(referenceGenome, intervalList));
+
         wrapper.run(Collections.singletonList(inputBam), coverageOut.getPath(), referenceGenome.getWorkingFastaFile(), extraArgs, true);
         if (!coverageOut.exists())
         {

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

@@ -136,17 +136,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 //GATK4 now requires intervals:
                 File intervalList = new File(ctx.getOutputDir(), "depthOfCoverageIntervals.intervals");
                 ctx.getFileManager().addIntermediateFile(intervalList);
-                try (PrintWriter writer = PrintWriters.getPrintWriter(intervalList))
-                {
-                    SAMSequenceDictionaryExtractor.extractDictionary(rg.getSequenceDictionary().toPath()).getSequences().forEach(x -> writer.println(x.getSequenceName()));
-                }
-                catch (IOException e)
-                {
-                    throw new PipelineJobException(e);
-                }
-
-                extraArgs.add("-L");
-                extraArgs.add(intervalList.getPath());
+                extraArgs.addAll(DepthOfCoverageWrapper.generateIntervalArgsForFullGenome(rg, intervalList));
             }
 
             Integer mmq = ctx.getParams().optInt("mmq");