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1) Make sure that the table size is set correctly in finalize() 

2) Make sure variants are biallelic before asking for isTransversion()



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4016 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-08-11 20:32:22 +00:00
parent 41d57b7139
commit 8c08f47923
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
View File

@ -78,7 +78,7 @@ class TiTvRatioSample extends SampleDataPoint {
}
public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( vc != null && vc.isSNP() ) {
if ( vc != null && vc.isSNP() && vc.isBiallelic() ) {
if ( VariantContextUtils.isTransition(vc) ) {
nTi++;
} else {

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
View File

@ -163,7 +163,7 @@ class EvalBySample implements TableType {
}
public void finalizeTable() {
finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.size()];
finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.firstEntry().getValue().size()];
int i = 0;
for ( Map.Entry<String,List<SampleDataPoint>> evalBySample : sampleAndEvalResults.entrySet() ) {
int j = 0;