Support GATK SVAnnotateStep

Author: bbimber

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

@@ -113,6 +113,7 @@
 import org.labkey.sequenceanalysis.run.util.FastqcRunner;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBAppendHandler;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBImportHandler;
+import org.labkey.sequenceanalysis.run.util.SVAnnotateStep;
 import org.labkey.sequenceanalysis.run.variant.*;
 import org.labkey.sequenceanalysis.util.Barcoder;
 import org.labkey.sequenceanalysis.util.ChainFileValidator;
@@ -300,6 +301,7 @@ 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 SVAnnotateStep.Provider());
 
         //handlers
         SequenceAnalysisService.get().registerFileHandler(new LiftoverHandler());

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java

@@ -53,7 +53,7 @@ public StarWrapper(@Nullable Logger logger)
 
     public static class StarAlignmentStep extends AbstractAlignmentPipelineStep<StarWrapper> implements AlignmentStep
     {
-        public StarAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx)
+        public StarAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx)
         {
             super(provider, ctx, new StarWrapper(ctx.getLogger()));
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SVAnnotateStep.java

@@ -0,0 +1,104 @@
+package org.labkey.sequenceanalysis.run.util;
+
+import htsjdk.samtools.util.Interval;
+import org.apache.logging.log4j.Logger;
+import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJobException;
+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.ToolParameterDescriptor;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
+import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
+
+import javax.annotation.Nullable;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class SVAnnotateStep extends AbstractCommandPipelineStep<SVAnnotateStep.SNAnnotateWrapper> implements VariantProcessingStep
+{
+    public static final String GENE_PARAM = "gene_file";
+
+    public SVAnnotateStep(PipelineStepProvider<?> provider, PipelineContext ctx)
+    {
+        super(provider, ctx, new SNAnnotateWrapper(ctx.getLogger()));
+    }
+
+    public static class Provider extends AbstractVariantProcessingStepProvider<SVAnnotateStep>
+    {
+        public Provider()
+        {
+            super("SVAnnotateStep", "GATK SVAnnotate", "GATK", "This will run GATK's SVAnnotate to classify SVs by impact", Arrays.asList(
+                    ToolParameterDescriptor.createExpDataParam(GENE_PARAM, "Gene File", "This is the ID of a GTF or GFF3 file containing genes from this genome.", "sequenceanalysis-genomefileselectorfield", new JSONObject()
+                    {{
+                        put("extensions", Arrays.asList("gtf"));
+                        put("width", 400);
+                        put("allowBlank", false);
+                    }}, null)
+            ), PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js"), "");
+
+        }
+
+        @Override
+        public SVAnnotateStep create(PipelineContext ctx)
+        {
+            return new SVAnnotateStep(this, ctx);
+        }
+    }
+
+    @Override
+    public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List<Interval> intervals) throws PipelineJobException
+    {
+        VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
+
+        output.addInput(inputVCF, "Input VCF");
+        output.addInput(genome.getWorkingFastaFile(), "Reference Genome");
+
+        List<String> args = new ArrayList<>(getWrapper().getBaseArgs("SVAnnotate"));
+        args.add("-V");
+        args.add(inputVCF.getPath());
+
+        if (intervals != null)
+        {
+            intervals.forEach(interval -> {
+                args.add("-L");
+                args.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
+            });
+        }
+
+        Integer geneFileId = getProvider().getParameterByName(GENE_PARAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class);
+        File geneFile = getPipelineCtx().getSequenceSupport().getCachedData(geneFileId);
+        if (!geneFile.exists())
+        {
+            throw new PipelineJobException("Unable to find file: " + geneFile.getPath());
+        }
+        args.add("--protein-coding-gtf");
+        args.add(geneFile.getPath());
+
+        File outputVcf = new File(outputDirectory, SequenceTaskHelper.getUnzippedBaseName(inputVCF) + ".svannotate.vcf.gz");
+        getWrapper().execute(args);
+        if (!outputVcf.exists())
+        {
+            throw new PipelineJobException("output not found: " + outputVcf);
+        }
+
+        output.setVcf(outputVcf);
+
+        return output;
+    }
+
+    public static class SNAnnotateWrapper extends AbstractGatk4Wrapper
+    {
+        public SNAnnotateWrapper(@Nullable Logger logger)
+        {
+            super(logger);
+        }
+    }
+}

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

@@ -33,7 +33,7 @@ public class SelectSNVsStep extends AbstractCommandPipelineStep<SelectVariantsWr
     public static String SELECT_TYPE_TO_INCLUDE = "selectType";
     public static String SELECT_TYPE_TO_EXCLUDE = "selectTypeToExclude";
 
-    public SelectSNVsStep(PipelineStepProvider provider, PipelineContext ctx)
+    public SelectSNVsStep(PipelineStepProvider<?> provider, PipelineContext ctx)
     {
         super(provider, ctx, new SelectVariantsWrapper(ctx.getLogger()));
     }