Update all VariantAnnotator steps to use DISCVRseq wrapper

Author: bbimber

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

@@ -1,9 +1,8 @@
 package org.labkey.sequenceanalysis.run.util;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.pipeline.PipelineJobException;
-import org.labkey.api.sequenceanalysis.run.AbstractGatkWrapper;
+import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -12,7 +11,7 @@
 /**
  * Created by bimber on 8/8/2014.
  */
-public class VariantAnnotatorWrapper extends AbstractGatkWrapper
+public class VariantAnnotatorWrapper extends AbstractDiscvrSeqWrapper
 {
     public VariantAnnotatorWrapper(Logger log)
     {
@@ -21,20 +20,19 @@ public VariantAnnotatorWrapper(Logger log)
 
     public void execute(File referenceFasta, File inputVcf, File outputVcf, List<String> options) throws PipelineJobException
     {
-        getLogger().info("Running GATK VariantAnnotator");
+        getLogger().info("Running DiscvrVariantAnnotator");
 
         ensureDictionary(referenceFasta);
 
         List<String> args = new ArrayList<>(getBaseArgs());
-        args.add("-T");
-        args.add("VariantAnnotator");
+        args.add("DiscvrVariantAnnotator");
         args.add("-R");
         args.add(referenceFasta.getPath());
 
         args.add("-V");
         args.add(inputVcf.getPath());
 
-        args.add("-o");
+        args.add("-O");
         args.add(outputVcf.getPath());
 
         if (options != null)

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

@@ -100,16 +100,9 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             options.add("-A");
             options.add("GenotypeConcordanceBySite");
 
-            options.add("-resource:GT_SOURCE");
+            options.add("-rg");
             options.add(refVCF.getPath());
 
-            Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
-            if (threads != null)
-            {
-                options.add("-nt");
-                options.add(String.valueOf(Math.min(threads, 8)));
-            }
-
             if (intervals != null)
             {
                 intervals.forEach(interval -> {

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

@@ -88,13 +88,6 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             options.add("MinorAlleleFrequency");
         }
 
-        Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
-        if (threads != null)
-        {
-            options.add("-nt");
-            options.add(String.valueOf(Math.min(threads, 8)));
-        }
-
         if (intervals != null)
         {
             intervals.forEach(interval -> {
@@ -103,14 +96,6 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             });
         }
 
-         //TODO: allow annotation using fields from another VCF:
-        /**
-         -resource:indian "$INDIAN_SUBSET" \
-         -E indian.AF \
-         -resource:chinese "$CHINESE_SUBSET" \
-         -E chinese.AF \
-         */
-
         getWrapper().execute(genome.getWorkingFastaFile(), inputVCF, outputVcf, options);
         if (!outputVcf.exists())
         {