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Better printing support for false positives and false negatives in concordance tables 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2514 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-01-06 15:02:40 +00:00
parent 592749a7c1
commit 34519b3e3b
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
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@ -100,6 +100,12 @@ public class ConcordanceTruthTable {
int callType = getGenotype(evalG, ref);
//System.out.printf("TEST: %d/%d %s vs. %s%n", truthIndex, callIndex, chip, eval);
if ( truthType == VARIANT && callType != VARIANT ) {
violation = String.format("False negative: ref=%c chip=%s call=%s", ref, chipG, evalG);
} else if ( truthType == REF && callType == VARIANT ) {
violation = String.format("False positive: chip=%s call=%s", chipG, evalG);
}
addGenotypeEntry(truthType, callType);
}
} else { // if we cannot associate tables with individuals, then we are working in a pooled context