From 3530ef5a4159ba1b7555a46866b9a9b39efa85af Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 6 Apr 2010 15:02:56 +0000 Subject: [PATCH] Explicit type cast fixed in order to work with new ROD implementation git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index 41096aa5d..e71cd4d0f 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -604,7 +604,7 @@ public class IndelGenotyperV2Walker extends ReadWalker { else b.append(annUnknown); // we have no idea what this is. this may actually happen when we have a fully non-coding exon... } b.append('\t'); - b.append(((Transcript)ann.get(0)).getGeneName()); // there is at least one transcript in the list, guaranteed + b.append(((Transcript)ann.get(0).getUnderlyingObject()).getGeneName()); // there is at least one transcript in the list, guaranteed // while ( it.hasNext() ) { // // t.getGeneName() // }