Add BcftoolsSetGtStep

Author: bbimber

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

@@ -302,6 +302,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new MendelianViolationReportStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new SummarizeGenotypeQualityStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new BcftoolsFillTagsStep.Provider());
+        SequencePipelineService.get().registerPipelineStep(new BcftoolsSetGtStep.Provider());
         SequencePipelineService.get().registerPipelineStep(new SVAnnotateStep.Provider());
 
         //handlers

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

@@ -0,0 +1,116 @@
+package org.labkey.sequenceanalysis.run.analysis;
+
+import htsjdk.samtools.util.Interval;
+import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.BcftoolsRunner;
+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.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
+import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class BcftoolsSetGtStep extends AbstractCommandPipelineStep<BcftoolsRunner> implements VariantProcessingStep
+{
+    public BcftoolsSetGtStep(PipelineStepProvider<?> provider, PipelineContext ctx)
+    {
+        super(provider, ctx, new BcftoolsRunner(ctx.getLogger()));
+    }
+
+    public static class Provider extends AbstractVariantProcessingStepProvider<BcftoolsSetGtStep> implements SupportsScatterGather
+    {
+        public Provider()
+        {
+            super("BcftoolsSetGtStep", "Bcftools Set GT", "bcftools", "Can be used to convert single dot ('.') genotypes to './.' for compatibility with more tools.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public BcftoolsSetGtStep create(PipelineContext ctx)
+        {
+            return new BcftoolsSetGtStep(this, ctx);
+        }
+    }
+
+    @Override
+    public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List<Interval> intervals) throws PipelineJobException
+    {
+        VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
+
+        List<String> options = new ArrayList<>();
+        options.add(BcftoolsRunner.getBcfToolsPath().getPath());
+        options.add("+setGT");
+
+        options.add(inputVCF.getPath());
+
+        if (intervals != null)
+        {
+            options.add("--regions");
+            options.add(intervals.stream().map(interval -> interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd()).collect(Collectors.joining(",")));
+        }
+
+        options.add("-O");
+        options.add("z9");
+
+        Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
+        if (threads != null)
+        {
+            options.add("--threads");
+            options.add(threads.toString());
+        }
+
+        File outputVcf = new File(outputDirectory, SequenceTaskHelper.getUnzippedBaseName(inputVCF) + ".ft.vcf.gz");
+        options.add("-o");
+        options.add(outputVcf.getPath());
+
+        options.add("--");
+
+        options.add("-t");
+        options.add(".");
+
+        options.add("-n");
+        options.add("./.");
+
+        BcftoolsRunner wrapper = getWrapper();
+
+        String bcfPluginDir = StringUtils.trimToNull(System.getenv("BCFTOOLS_PLUGINS"));
+        if (bcfPluginDir != null)
+        {
+            getPipelineCtx().getLogger().debug("Setting BCFTOOLS_PLUGINS environment variable: " + bcfPluginDir);
+            wrapper.addToEnvironment("BCFTOOLS_PLUGINS", bcfPluginDir);
+        }
+
+        wrapper.execute(options);
+        if (!outputVcf.exists())
+        {
+            throw new PipelineJobException("output not found: " + outputVcf);
+        }
+
+        try
+        {
+            SequenceAnalysisService.get().ensureVcfIndex(outputVcf, getWrapper().getLogger());
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
+
+        output.setVcf(outputVcf);
+
+        return output;
+    }
+}