From 88ffb08af44b93d3727f590bdc7a0d54eba026de Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 16 Jul 2009 02:31:10 +0000 Subject: [PATCH] Need to return real values for some of the AllelicVariant methods git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1264 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/rodVariants.java | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java index 3c39f11ad..5c166180d 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java @@ -148,9 +148,16 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa return new String( b ); } - public char getRefSnpFWD() throws IllegalStateException { return 0; } - public String getAltBasesFWD() { return null; } - public char getAltSnpFWD() throws IllegalStateException { return 0; } + public char getRefSnpFWD() throws IllegalStateException { return getReferenceBase(); } + public String getAltBasesFWD() { return getBestGenotype(); } + public char getAltSnpFWD() throws IllegalStateException { + String bases = getBestGenotype(); + if ( bases.charAt(0) != getRefSnpFWD() ) + return bases.charAt(0); + else + return bases.charAt(1); + + } public boolean isReference() { return ! isSNP(); } public boolean isSNP() { return getLodBtr() > 5; } public boolean isInsertion() { return false; }