From feb7238f102d67a4ddf653c81f95a63c96c464d0 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 30 Jul 2009 03:08:04 +0000 Subject: [PATCH] Wasn't always returning the correct alt base git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java index a979626d4..8672460e7 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java @@ -24,7 +24,11 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes { public String getRefBasesFWD() { return this.get("2"); } public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); } public String getAltBasesFWD() { return this.get("3"); } - public char getAltSnpFWD() throws IllegalStateException { return getAltBasesFWD().charAt(0); } + public char getAltSnpFWD() throws IllegalStateException { + if ( getAltBasesFWD().charAt(0) != getRefSnpFWD() ) + return getAltBasesFWD().charAt(0); + return getAltBasesFWD().charAt(1); + } public boolean isReference() { return getVariationConfidence() < 0.01; } public boolean isSNP() { return ! isReference(); } public boolean isInsertion() { return false; }