Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java

@@ -141,6 +141,11 @@ public class GATKArgumentCollection {
     @Argument(fullName = "interval_merging", shortName = "im", doc = "What interval merging rule should we use {ALL [DEFAULT],OVERLAPPING_ONLY,NONE}.", required = false)
     public INTERVAL_MERGING_RULE intervalMerging = INTERVAL_MERGING_RULE.ALL;
 
+    /** Should we enable rodWalkers?  This is currently unsafe */
+    @Element(required = false)
+    @Argument(fullName = "enableRodWalkers", shortName = "erw", doc = "Enable experimental rodWalker support.  TEMPORARY HACK TO ALLOW EXPERIMENTATION WITH ROD WALKERS.  [default is false]}.", required = false)
+    public boolean enableRodWalkers = false;
+
     /**
      * marshal the data out to a object
      *
@@ -294,6 +299,9 @@ public class GATKArgumentCollection {
         if (other.intervalMerging != this.intervalMerging) {
             return false;
         }
+        if (other.enableRodWalkers != this.enableRodWalkers) {
+            return false;
+        }
 
         return true;
     }

java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MergingIterator;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.*;
 
@@ -87,7 +88,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
 
         rodQueue = new MergingIterator<RODRecordList<ReferenceOrderedDatum>>(iterators);
 
-        throw new StingException("RodLocusView currently disabled");
+        //throw new StingException("RodLocusView currently disabled");
     }
 
     public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
@@ -127,7 +128,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
         // calculate the number of skipped bases, and update lastLoc so we can do that again in the next()
         long skippedBases = getSkippedBases( rodSite );
         lastLoc = site;
-        return new AlignmentContext(site, new ArrayList<SAMRecord>(), new ArrayList<Integer>(), skippedBases);
+        return new AlignmentContext(site, new ReadBackedPileup(site), skippedBases);
     }
     
     private RefMetaDataTracker createTracker( Collection<RODRecordList<ReferenceOrderedDatum>> allTracksHere ) {

java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.traversals;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.WalkerManager;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.providers.*;
@@ -13,6 +14,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;
 
@@ -21,7 +23,7 @@ import java.util.ArrayList;
  */
 public class TraverseLoci extends TraversalEngine {
     final private static String LOCI_STRING = "sites";
-    final private static boolean ENABLE_ROD_TRAVERSAL = false;
+    //final private static boolean ENABLE_ROD_TRAVERSAL = false;
 
 
     /**
@@ -57,7 +59,7 @@ public class TraverseLoci extends TraversalEngine {
 
             //ReferenceOrderedView referenceOrderedDataView = new ReferenceOrderedView( dataProvider );
             ReferenceOrderedView referenceOrderedDataView = null;
-            if ( ! ENABLE_ROD_TRAVERSAL || WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE_ORDERED_DATA )
+            if ( ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers || WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE_ORDERED_DATA )
                 referenceOrderedDataView = new ManagingReferenceOrderedView( dataProvider );
             else
                 referenceOrderedDataView = (RodLocusView)locusView;
@@ -102,12 +104,13 @@ public class TraverseLoci extends TraversalEngine {
 
             // We have a final map call to execute here to clean up the skipped based from the
             // last position in the ROD to that in the interval
-        if ( ENABLE_ROD_TRAVERSAL && WalkerManager.getWalkerDataSource(walker) == DataSource.REFERENCE_ORDERED_DATA ) {
+        if ( GenomeAnalysisEngine.instance.getArguments().enableRodWalkers && WalkerManager.getWalkerDataSource(walker) == DataSource.REFERENCE_ORDERED_DATA ) {
             RodLocusView rodLocusView = (RodLocusView)locusView;
             long nSkipped = rodLocusView.getLastSkippedBases();
             if ( nSkipped > 0 ) {
                 // no sense in making the call if you don't have anything interesting to say
-                AlignmentContext ac = new AlignmentContext(rodLocusView.getLocOneBeyondShard(), null, null, nSkipped);
+                GenomeLoc site = rodLocusView.getLocOneBeyondShard();
+                AlignmentContext ac = new AlignmentContext(site, new ReadBackedPileup(site), nSkipped);
                 M x = locusWalker.map(null, null, ac);
                 sum = locusWalker.reduce(x, sum);
             }
@@ -135,7 +138,7 @@ public class TraverseLoci extends TraversalEngine {
         DataSource dataSource = WalkerManager.getWalkerDataSource(walker);
         if( dataSource == DataSource.READS )
             return new CoveredLocusView(dataProvider);
-        else if( dataSource == DataSource.REFERENCE || ! ENABLE_ROD_TRAVERSAL )
+        else if( dataSource == DataSource.REFERENCE || ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers )
             return new AllLocusView(dataProvider);
         else if( dataSource == DataSource.REFERENCE_ORDERED_DATA )
             return new RodLocusView(dataProvider);

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -22,8 +22,8 @@ import java.util.*;
  */
 @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
 //@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
-public class VariantEvalWalker extends RefWalker<Integer, Integer> {
+//public class VariantEvalWalker extends RefWalker<Integer, Integer> {
-//public class VariantEvalWalker extends RodWalker<Integer, Integer> {
+public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     @Argument(shortName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
     public double minConfidenceScore = -1.0;
 

java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java

@@ -177,7 +177,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
 	public void testEvalRuntimeWithLotsOfIntervals() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("");
+        md5.add("d11ea079fc1835514d392056a2c2a28d");
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T VariantEval -R " + oneKGLocation + "reference/human_b36_both.fasta " +
                 "-B eval,Variants," + validationDataLocation + "NA12878.pilot_3.all.geli.calls " +