Support SummarizeGenotypeQuality tool

Author: bbimber

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

@@ -137,6 +137,7 @@
 import org.labkey.sequenceanalysis.run.variant.SelectSNVsStep;
 import org.labkey.sequenceanalysis.run.variant.SelectSamplesStep;
 import org.labkey.sequenceanalysis.run.variant.SelectVariantsStep;
+import org.labkey.sequenceanalysis.run.variant.SummarizeGenotypeQualityStep;
 import org.labkey.sequenceanalysis.run.variant.VariantAnnotatorStep;
 import org.labkey.sequenceanalysis.run.variant.VariantEvalBySampleStep;
 import org.labkey.sequenceanalysis.run.variant.VariantEvalStep;
@@ -320,6 +321,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new VariantQCStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new PlinkPcaStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new MendelianViolationReportStep.Provider());
+        SequencePipelineService.get().registerPipelineStep(new SummarizeGenotypeQualityStep.Provider());
 
         //handlers
         SequenceAnalysisService.get().registerFileHandler(new LiftoverHandler());

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

@@ -0,0 +1,89 @@
+package org.labkey.sequenceanalysis.run.variant;
+
+import htsjdk.samtools.util.Interval;
+import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
+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.pipeline.ToolParameterDescriptor;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
+import org.labkey.api.sequenceanalysis.run.DISCVRSeqRunner;
+
+import javax.annotation.Nullable;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * User: bimber
+ * Date: 6/15/2014
+ * Time: 12:39 PM
+ */
+public class SummarizeGenotypeQualityStep extends AbstractPipelineStep implements VariantProcessingStep
+{
+    public SummarizeGenotypeQualityStep(PipelineStepProvider<?> provider, PipelineContext ctx)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractVariantProcessingStepProvider<SummarizeGenotypeQualityStep> implements RequiresPedigree
+    {
+        public Provider()
+        {
+            super("SummarizeGenotypeQuality", "Summarize Genotype Quality", "DISCVRseq", "This produces a TSV report summarizing genotype qualities by Genotype Type", Arrays.asList(
+                    ToolParameterDescriptor.create("excludeFiltered", "Exclude Filtered", "If selected, filtered sites will be ignored.", "checkbox", new JSONObject(){{
+                        put("checked", false);
+                    }}, null)
+                ), null, "");
+        }
+
+        public SummarizeGenotypeQualityStep create(PipelineContext ctx)
+        {
+            return new SummarizeGenotypeQualityStep(this, ctx);
+        }
+    }
+
+    @Override
+    public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List<Interval> intervals) throws PipelineJobException
+    {
+        VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
+
+        DISCVRSeqRunner wrapper = new DISCVRSeqRunner(getPipelineCtx().getLogger());
+        List<String> args = new ArrayList<>(wrapper.getBaseArgs("SummarizeGenotypeQuality"));
+
+        if (getProvider().getParameterByName("excludeFiltered").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false))
+        {
+            args.add("--excludeFiltered");
+        }
+
+        if (intervals != null)
+        {
+            intervals.forEach(interval -> {
+                args.add("-L");
+                args.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
+            });
+        }
+
+        args.add("-V");
+        args.add(inputVCF.getPath());
+
+        File outputTable = new File(outputDirectory, SequencePipelineService.get().getUnzippedBaseName(inputVCF.getName()) + ".gq.txt");
+        args.add("-O");
+        args.add(outputTable.getPath());
+
+        wrapper.execute(args);
+
+        output.addInput(inputVCF, "Input VCF");
+        output.addOutput(outputTable, "Genotype Quality Summary");
+
+        output.addSequenceOutput(outputTable, "Genotype Quality Summary for: " + inputVCF.getName(), "Genotype Quality Summary", null, null, genome.getGenomeId(), null);
+
+        return output;
+    }
+}