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Moving over to VariantContext 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-15 22:07:28 +00:00
parent 7adff5b81a
commit 02a6f4c401
1 changed files with 17 additions and 14 deletions
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31
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariationRod;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -20,7 +19,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Iterator;
/** /**
* Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 and MQ0 reads. * Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 and MQ0 reads.
@ -75,18 +73,23 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
// look at the rods for indels or SNPs // look at the rods for indels or SNPs
if ( tracker != null ) { if ( tracker != null ) {
Iterator<GATKFeature> rods = tracker.getAllRods().iterator(); for ( VariantContext vc : tracker.getAllVariantContexts() ) {
while ( rods.hasNext() ) { switch ( vc.getType() ) {
Object rod = rods.next().getUnderlyingObject(); case INDEL:
if ( rod instanceof VariationRod ) { hasIndel = true;
if ( ((VariationRod)rod).isIndel() ) { if ( vc.isInsertion() )
hasIndel = true;
if ( ((VariationRod)rod).isInsertion() )
hasInsertion = true; hasInsertion = true;
} break;
if ( ((VariationRod)rod).isSNP() ) case SNP:
hasPointEvent = true; hasPointEvent = true;
} break;
case MIXED:
hasPointEvent = true;
hasIndel = true;
if ( vc.isInsertion() )
hasInsertion = true;
break;
}
} }
} }