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Need to check for biallelic snp or exception gets thrown. 

Also, update to new tracker calls.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1913 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-27 02:43:43 +00:00
parent 3fb3773098
commit e96b1791ab
2 changed files with 21 additions and 11 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java
View File

@ -2,6 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RODRecordList;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Variation;
@ -52,8 +54,10 @@ public class SNPGenotypeConcordance implements ConcordanceType {
}
public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
Variation call1 = (Variation)tracker.lookup("callset1", null);
Variation call2 = (Variation)tracker.lookup("callset2", null);
RODRecordList<ReferenceOrderedDatum> call1List = tracker.getTrackData("callset1", null);
RODRecordList<ReferenceOrderedDatum> call2List = tracker.getTrackData("callset2", null);
Variation call1 = (call1List == null ? null : (Variation)call1List.getRecords().get(0));
Variation call2 = (call2List == null ? null : (Variation)call2List.getRecords().get(0));
// the only reason they would be null is a lack of coverage
if ( call1 == null || call2 == null ) {

24
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java
View File

@ -2,6 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RODRecordList;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.Variation;
@ -38,8 +40,10 @@ public class SimpleVenn implements ConcordanceType {
}
public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
Variation call1 = (Variation)tracker.lookup("callset1", null);
Variation call2 = (Variation)tracker.lookup("callset2", null);
RODRecordList<ReferenceOrderedDatum> call1List = tracker.getTrackData("callset1", null);
RODRecordList<ReferenceOrderedDatum> call2List = tracker.getTrackData("callset2", null);
Variation call1 = (call1List == null ? null : (Variation)call1List.getRecords().get(0));
Variation call2 = (call2List == null ? null : (Variation)call2List.getRecords().get(0));
if ( call1 == null && call2 == null )
return;
@ -55,13 +59,15 @@ public class SimpleVenn implements ConcordanceType {
else if ( call1 == null )
printVariant(set2_writer, call2);
// intersection (concordant)
else if ( call1.getAlternativeBaseForSNP() == call2.getAlternativeBaseForSNP())
printVariant(intersect_writer, call1);
// intersection (discordant)
else
printVariant(discord_writer, call1);
// we can't really deal with multi-allelic variants
else if ( call1.isBiallelic() && call2.isBiallelic() ) {
// intersection (concordant)
if ( call1.getAlternativeBaseForSNP() == call2.getAlternativeBaseForSNP() )
printVariant(intersect_writer, call1);
// intersection (discordant)
else
printVariant(discord_writer, call1);
}
}
private static void printVariant(PrintWriter writer, Variation variant) {