From 34519b3e3b71ba2f76c3d24a40637a033818c12f Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 6 Jan 2010 15:02:40 +0000 Subject: [PATCH] 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 --- .../gatk/walkers/varianteval/ConcordanceTruthTable.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java index efa300559..aec483712 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java @@ -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