Automatically index VariantFiltration mask files

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -61,8 +61,6 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public void registerReadsetHandler(SequenceOutputHandler<SequenceOutputHandler.SequenceReadsetProcessor> handler);
 
-    //abstract public File createTabixIndex(File input, @Nullable Logger log) throws PipelineJobException;
-
     abstract public void registerDataProvider(SequenceDataProvider p);
 
     abstract public List<NavItem> getNavItems(Container c, User u, SequenceDataProvider.SequenceNavItemCategory category);
@@ -102,4 +100,6 @@ static public void setInstance(SequenceAnalysisService instance)
     abstract public String getScriptPath(String moduleName, String path) throws PipelineJobException;
 
     abstract public void sortGxf(Logger log, File input, @Nullable File output) throws PipelineJobException;
+
+    abstract public void ensureFeatureFileIndex(File input, Logger log) throws PipelineJobException;
 }

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

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis;
 
+import htsjdk.samtools.util.FileExtensions;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
@@ -47,6 +48,7 @@
 import org.labkey.sequenceanalysis.run.util.BgzipRunner;
 import org.labkey.sequenceanalysis.run.util.FastaIndexer;
 import org.labkey.sequenceanalysis.run.util.GxfSorter;
+import org.labkey.sequenceanalysis.run.util.IndexFeatureFileWrapper;
 import org.labkey.sequenceanalysis.run.util.TabixRunner;
 import org.labkey.sequenceanalysis.util.ReferenceLibraryHelperImpl;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
@@ -485,4 +487,36 @@ public void sortGxf(Logger log, File input, @Nullable File output) throws Pipeli
     {
         new GxfSorter(log).sortGxf(input, output);
     }
+
+    @Override
+    public void ensureFeatureFileIndex(File input, Logger log) throws PipelineJobException
+    {
+        if (SequenceUtil.FILETYPE.bed.getFileType().isType(input))
+        {
+            File expected = new File(input.getPath() + FileExtensions.TRIBBLE_INDEX);
+            if (expected.exists())
+            {
+                log.debug("index exists: " + expected.getPath());
+            }
+            else
+            {
+                new IndexFeatureFileWrapper(log).ensureFeatureFileIndex(input);
+            }
+        }
+        else if (SequenceUtil.FILETYPE.vcf.getFileType().isType(input))
+        {
+            try
+            {
+                ensureVcfIndex(input, log);
+            }
+            catch (IOException e)
+            {
+                throw new PipelineJobException(e);
+            }
+        }
+        else
+        {
+            throw new IllegalArgumentException("Unexpected input file type, cannot index: " + input.getName());
+        }
+    }
 }

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

@@ -0,0 +1,26 @@
+package org.labkey.sequenceanalysis.run.util;
+
+import org.apache.log4j.Logger;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+public class IndexFeatureFileWrapper extends AbstractGatk4Wrapper
+{
+    public IndexFeatureFileWrapper(Logger log)
+    {
+        super(log);
+    }
+
+    public void ensureFeatureFileIndex(File input) throws PipelineJobException
+    {
+        List<String> args1 = new ArrayList<>(getBaseArgs());
+        args1.add("IndexFeatureFile");
+        args1.add("-I");
+        args1.add(input.getPath());
+        execute(args1);
+    }
+}

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

@@ -7,6 +7,7 @@
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.pipeline.PipelineJob;
 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.CommandLineParam;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
@@ -115,6 +116,9 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             {
                 throw new PipelineJobException("file not found for dataId: " + mask.opt("fileId"));
             }
+
+            SequenceAnalysisService.get().ensureFeatureFileIndex(maskData, getPipelineCtx().getLogger());
+
             params.add(maskData.getPath());
         }