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Moving over to VariationContext in CountCovariates. Removed references to class Variation. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3199 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-04-20 13:26:22 +00:00
parent 1bc26f69e9
commit 00feb3eee0
1 changed files with 5 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
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.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.classloader.PackageUtils;
@ -36,7 +36,6 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -250,13 +249,13 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
// Pull out data for this locus for all the input RODs and check if this is a known variant site in any of them // Pull out data for this locus for all the input RODs and check if this is a known variant site in any of them
boolean isSNP = false; boolean isSNP = false;
for( GATKFeature rod : tracker.getAllRods() ) { for( final VariantContext vc : tracker.getAllVariantContexts(ref, null, context.getLocation(), false, false) ) {
if( rod != null && rod.getUnderlyingObject() instanceof Variation && ((Variation)rod.getUnderlyingObject()).isSNP() ) { if( vc != null && vc.isSNP() ) {
isSNP = true; // At least one of the rods says this is a snp site isSNP = true;
break; break;
} }
} }
// Only use data from non-dbsnp sites // Only use data from non-dbsnp sites
// Assume every mismatch at a non-dbsnp site is indicative of poor quality // Assume every mismatch at a non-dbsnp site is indicative of poor quality
if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) { if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) {