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update this walker so any variants can be passed in 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1426 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-17 16:30:39 +00:00
parent 8403618846
commit df5744bcd3
1 changed files with 3 additions and 7 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
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@ -9,9 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@WalkerName("SNPClusters") @WalkerName("SNPClusters")
@By(DataSource.REFERENCE) @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)})
@Requires(DataSource.REFERENCE)
@Allows(DataSource.REFERENCE)
public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> { public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false) @Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false)
int windowSize = 10; int windowSize = 10;
@ -22,10 +20,8 @@ public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
} }
public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null); AllelicVariant snp = (AllelicVariant)tracker.lookup("snps", null);
if ( eval instanceof SNPCallFromGenotypes ) return (snp != null && snp.isSNP()) ? context.getLocation() : null;
return context.getLocation();
return null;
} }
public void onTraversalDone(GenomeLoc sum) { public void onTraversalDone(GenomeLoc sum) {