support lofreq's indelqual step

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -93,6 +93,7 @@
 import org.labkey.sequenceanalysis.run.bampostprocessing.DiscardUnmappedReadsStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.FixMateInformationStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.IndelRealignerStep;
+import org.labkey.sequenceanalysis.run.bampostprocessing.LofreqIndelQualStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.MarkDuplicatesStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.MarkDuplicatesWithMateCigarStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.RnaSeQCStep;
@@ -264,6 +265,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new SortSamStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new SplitNCigarReadsStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new ClipOverlappingAlignmentsWrapper.ClipOverlappingAlignmentsStep.Provider());
+        SequencePipelineService.get().registerPipelineStep(new LofreqIndelQualStep.Provider());
 
         //analysis
         SequencePipelineService.get().registerPipelineStep(new SequenceBasedTypingAnalysis.Provider());

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

@@ -514,6 +514,32 @@ public File execute(File input, File outputVcf, File fasta, @Nullable Integer th
             return outputVcf;
         }
 
+        public File addIndelQuals(File inputBam, File outputBam, File fasta) throws PipelineJobException
+        {
+            List<String> args = new ArrayList<>();
+            args.add(getExe().getPath());
+            args.add("indelqual");
+
+            args.add("--dindel");
+
+            args.add("--ref");
+            args.add(fasta.getPath());
+
+            args.add("--out");
+            args.add(outputBam.getPath());
+
+            args.add(inputBam.getPath());
+
+            execute(args);
+
+            if (!outputBam.exists())
+            {
+                throw new PipelineJobException("Unable to find file: " + outputBam.getPath());
+            }
+
+            return outputBam;
+        }
+
         private File getExe()
         {
             return SequencePipelineService.get().getExeForPackage("LOFREQPATH", "lofreq");

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

@@ -0,0 +1,54 @@
+package org.labkey.sequenceanalysis.run.bampostprocessing;
+
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.model.Readset;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.BamProcessingOutputImpl;
+import org.labkey.api.sequenceanalysis.pipeline.BamProcessingStep;
+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.SequencePipelineService;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
+import org.labkey.api.util.FileUtil;
+import org.labkey.sequenceanalysis.run.analysis.LofreqAnalysis;
+
+import java.io.File;
+import java.util.Collections;
+
+public class LofreqIndelQualStep extends AbstractCommandPipelineStep<LofreqAnalysis.LofreqWrapper> implements BamProcessingStep
+{
+    public LofreqIndelQualStep(PipelineStepProvider provider, PipelineContext ctx)
+    {
+        super(provider, ctx, new LofreqAnalysis.LofreqWrapper(ctx.getLogger()));
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<MarkDuplicatesStep>
+    {
+        public Provider()
+        {
+            super("LofreqIndelQual", "Lofreq Indelqual", "Lofreq", "This runs lofreq's indelqual, which adds indel qualities necessary to call somatic indels.", Collections.emptyList(), null, "http://csb5.github.io/lofreq/");
+        }
+
+        @Override
+        public MarkDuplicatesStep create(PipelineContext ctx)
+        {
+            return new MarkDuplicatesStep(this, ctx);
+        }
+    }
+
+    @Override
+    public Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGenome, File outputDirectory) throws PipelineJobException
+    {
+        BamProcessingOutputImpl output = new BamProcessingOutputImpl();
+        getWrapper().setOutputDir(outputDirectory);
+
+        File outputBam = new File(outputDirectory, FileUtil.getBaseName(inputBam) + ".lofreqindel.bam");
+        output.addIntermediateFile(outputBam);
+        output.setBAM(getWrapper().addIndelQuals(inputBam, outputBam, referenceGenome.getWorkingFastaFile()));
+
+        SequencePipelineService.get().ensureBamIndex(outputBam, getPipelineCtx().getLogger(), false);
+
+        return output;
+    }
+}