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Fixed import statements. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5145 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-31 19:26:37 +00:00
parent 4d9bc84bd5
commit 4cb910bc38
2 changed files with 7 additions and 6 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
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@ -18,7 +18,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.MendelianViolationEvaluator;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AlleleFrequencyComparison.java
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@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.report.utils.TableType;
@ -38,10 +38,11 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
public String getName() { return "Allele Frequency Comparison"; } public String getName() { return "Allele Frequency Comparison"; }
public AlleleFrequencyComparison(VariantEvalWalker parent) { public AlleleFrequencyComparison(VariantEvalWalker parent) {
super(parent); //super(parent);
} }
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) { //public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( ! (isValidVC(eval) && isValidVC(comp)) ) { if ( ! (isValidVC(eval) && isValidVC(comp)) ) {
return null; return null;
} else { } else {
@ -73,7 +74,7 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
Map<String,Object> attributes = new HashMap<String,Object>(); Map<String,Object> attributes = new HashMap<String,Object>();
VariantContextUtils.calculateChromosomeCounts(vc,attributes,false); VariantContextUtils.calculateChromosomeCounts(vc,attributes,false);
vc = VariantContext.modifyAttributes(vc,attributes); vc = VariantContext.modifyAttributes(vc,attributes);
getLogger().debug(String.format("%s %s | %s %s",attributes.get("AC"),attributes.get("AF"),vc.getAttribute("AC"),vc.getAttribute("AF"))); //getLogger().debug(String.format("%s %s | %s %s",attributes.get("AC"),attributes.get("AF"),vc.getAttribute("AC"),vc.getAttribute("AF")));
if ( attributes.size() == 2 && missingField(vc) ) { if ( attributes.size() == 2 && missingField(vc) ) {
throw new org.broadinstitute.sting.utils.exceptions.StingException("VariantContext should have had attributes modified but did not"); throw new org.broadinstitute.sting.utils.exceptions.StingException("VariantContext should have had attributes modified but did not");
} }