From 990af3f76e71547dbaad851796fcc1f14852b657 Mon Sep 17 00:00:00 2001 From: asivache Date: Mon, 1 Feb 2010 15:40:01 +0000 Subject: [PATCH] Will now work with simplest tabular format - genotype string ("+ACTT") does not have to be followed by ':' git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2755 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/refdata/SimpleIndelROD.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java index 2dbc6b4e5..440fb5671 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java @@ -33,7 +33,11 @@ public class SimpleIndelROD extends TabularROD implements VariationRod { return Arrays.asList(this.get("4")); String str = this.get("3"); - return Arrays.asList(str.substring(1, str.indexOf(":"))); + int pos = str.indexOf(":"); + if ( pos == -1 ) { + return Arrays.asList(str.substring(1)); + } + return Arrays.asList(str.substring(1, pos)); } public String getFWDRefBases() { return ""; }