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Added MNP to recognized and counted event types 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5266 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-02-17 22:37:38 +00:00
parent 57c66b5602
commit 7ffcade3c3
1 changed files with 7 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -33,6 +33,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
@DataPoint(description = "Number of snp loci") @DataPoint(description = "Number of snp loci")
public long nSNPs = 0; public long nSNPs = 0;
@DataPoint(description = "Number of mnp loci")
public long nMNPs = 0;
@DataPoint(description = "Number of insertions") @DataPoint(description = "Number of insertions")
public long nInsertions = 0; public long nInsertions = 0;
@DataPoint(description = "Number of deletions") @DataPoint(description = "Number of deletions")
@ -40,6 +42,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
@DataPoint(description = "Number of complex loci") @DataPoint(description = "Number of complex loci")
public long nComplex = 0; public long nComplex = 0;
@DataPoint(description = "Number of no calls loci") @DataPoint(description = "Number of no calls loci")
public long nNoCalls = 0; public long nNoCalls = 0;
@DataPoint(description = "Number of het loci") @DataPoint(description = "Number of het loci")
@ -97,6 +100,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
nSNPs++; nSNPs++;
if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++; if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
break; break;
case MNP:
nMNPs++;
if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
break;
case INDEL: case INDEL:
if (vc1.isInsertion()) nInsertions++; if (vc1.isInsertion()) nInsertions++;
else nDeletions++; else nDeletions++;