Ensure Lofreq BAM is coordinate sorted

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/LofreqIndelQualStep.java

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.run.bampostprocessing;
 
+import htsjdk.samtools.SAMFileHeader;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
@@ -8,12 +9,16 @@
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.SamSorter;
+import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.util.FileUtil;
 import org.labkey.sequenceanalysis.run.analysis.LofreqAnalysis;
+import picard.sam.SortSam;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Collections;
 
 public class LofreqIndelQualStep extends AbstractCommandPipelineStep<LofreqAnalysis.LofreqWrapper> implements BamProcessingStep
@@ -58,6 +63,18 @@ public Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGen
 
         output.setBAM(getWrapper().addIndelQuals(inputBam, outputBam, referenceGenome.getWorkingFastaFile()));
 
+        try
+        {
+            if (SequencePipelineService.get().getBamSortOrder(outputBam) != SAMFileHeader.SortOrder.coordinate)
+            {
+                new SamSorter(getWrapper().getLogger()).execute(outputBam, null, SAMFileHeader.SortOrder.coordinate);
+            }
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
+
         SequencePipelineService.get().ensureBamIndex(outputBam, getPipelineCtx().getLogger(), false);
 
         return output;