Removing more references to VCFRecord

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3789 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java

@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.vcf.VCFCodec;
-import org.broad.tribble.vcf.VCFRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
@@ -22,7 +22,7 @@ import java.util.*;
  * Time: 3:25:11 PM
  * To change this template use File | Settings | File Templates.
  */
-@Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="variants",type=VCFRecord.class)})
+@Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="variants",type=ReferenceOrderedDatum.class)})
 public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>, Map<String,Set<Double>>> {
 
 
@@ -47,13 +47,12 @@ public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>
     }
 
     public Map<String,Double> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        VCFRecord record = tracker.lookup("variants", VCFRecord.class);
+        VariantContext vc = tracker.getVariantContext(ref, "variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), false);
-
+        if ( vc == null || !vc.isBiallelic() ) {
-        if ( record == null ) {
             return null;
         }
 
-        return getAlleleBalanceBySample(record,ref,context);
+        return getAlleleBalanceBySample(vc,ref,context);
     }
 
     public void onTraversalDone(Map<String,Set<Double>> finalSets) {
@@ -67,13 +66,13 @@ public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>
         }
     }
 
-    private HashMap<String,Double> getAlleleBalanceBySample(VCFRecord vcf, ReferenceContext ref, AlignmentContext context) {
+    private HashMap<String,Double> getAlleleBalanceBySample(VariantContext vc, ReferenceContext ref, AlignmentContext context) {
         Map<String, StratifiedAlignmentContext> sampleContext = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(),null);
         HashMap<String,Double> balances = new HashMap<String,Double>();
         System.out.println("----- "+ref.getLocus()+" -----");
         int returnedBalances = 0;
-        for ( String sample : vcf.getSampleNames() ) {
+        for ( String sample : vc.getSampleNames() ) {
-            Double balance = getAlleleBalance(ref,sampleContext.get(sample),vcf.getAlternativeBaseForSNP());
+            Double balance = getAlleleBalance(ref,sampleContext.get(sample),(char)vc.getAlternateAllele(0).getBases()[0]);
             balances.put(sample, balance);
             if ( balance != null ) {
                 returnedBalances++;

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java

@@ -25,23 +25,23 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
 
-import org.broad.tribble.vcf.VCFCodec;
-import org.broad.tribble.vcf.VCFRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
 
+import java.util.EnumSet;
+
 /**
  * Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display
  */
 @By(DataSource.REFERENCE)
-@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class))
+@Requires(value={},referenceMetaData=@RMD(name="eval",type=ReferenceOrderedDatum.class))
 public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDensity.Counter> {
     @Argument(fullName="granularity", shortName="granularity", doc="", required=false)
     private int granularity = 1000000;
@@ -63,11 +63,7 @@ public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDe
     }
 
     public Pair<VariantContext, GenomeLoc> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        VariantContext vc = null;
+        VariantContext vc = tracker.getVariantContext(ref, "eval", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), false);
-
-        VCFRecord vcf = tracker.lookup("eval",VCFRecord.class);
-        if (vcf != null)
-            vc = VariantContextAdaptors.toVariantContext("eval", vcf, ref);
         return new Pair<VariantContext, GenomeLoc>(vc, context.getLocation());
     }