From 73ddf21bb775b659365ab3603aa23d9ee5a04244 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 27 Jul 2009 15:20:43 +0000 Subject: [PATCH] SNPs no longer fail this filter if they are actually hom in reads git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1319 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/variants/VECFisherStrand.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java index 8eb53b5bc..88b0f0651 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java @@ -32,6 +32,8 @@ public class VECFisherStrand implements VariantExclusionCriterion { public static boolean strandTest(char ref, LocusContext context, int allele1, int allele2, double threshold, StringBuffer out) { int[][] table = getContingencyTable(context, allele1, allele2); + if ( !variantIsHet(table) ) + return false; double pCutoff = computePValue(table); //printTable(table, pCutoff); @@ -75,6 +77,10 @@ public class VECFisherStrand implements VariantExclusionCriterion { return pValue < threshold; } + private static boolean variantIsHet(int[][] table) { + return ((table[0][1] != 0 || table[0][1] != 0) && (table[1][0] != 0 || table[1][1] != 0)); + } + private void printTable(int[][] table, double pValue) { System.out.printf("%d %d; %d %d : %f\n", table[0][0], table[0][1], table[1][0], table[1][1], pValue); }