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Removing more references to VCFRecord 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3789 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-14 11:54:23 +00:00
parent a4f8d70d8d
commit af23762778
2 changed files with 14 additions and 19 deletions
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19
java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
View File

@ -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);
if ( record == null ) {
VariantContext vc = tracker.getVariantContext(ref, "variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), false);
if ( vc == null || !vc.isBiallelic() ) {
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() ) {
Double balance = getAlleleBalance(ref,sampleContext.get(sample),vcf.getAlternativeBaseForSNP());
for ( String sample : vc.getSampleNames() ) {
Double balance = getAlleleBalance(ref,sampleContext.get(sample),(char)vc.getAlternateAllele(0).getBases()[0]);
balances.put(sample, balance);
if ( balance != null ) {
returnedBalances++;

14
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
View File

@ -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;
VCFRecord vcf = tracker.lookup("eval",VCFRecord.class);
if (vcf != null)
vc = VariantContextAdaptors.toVariantContext("eval", vcf, ref);
VariantContext vc = tracker.getVariantContext(ref, "eval", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), false);
return new Pair<VariantContext, GenomeLoc>(vc, context.getLocation());
}