From 35382468eec36597126bccb152963cca0962cd23 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Nov 2010 16:36:34 +0000
Subject: [PATCH] Better error checking/output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4676 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../features/annotator/AnnotatorInputTableCodec.java       | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
index e87986a2e..903133ffa 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
@@ -92,10 +92,13 @@ public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec<
 
         GenomeLoc loc;
         String chr = st.nextToken();
-        if ( chr.indexOf(":") != -1 )
+        if ( chr.indexOf(":") != -1 ) {
             loc = genomeLocParser.parseGenomeInterval(chr);
-        else
+        } else {
+            if ( st.countTokens() < 3 )
+                throw new CodecLineParsingException("Couldn't parse GenomeLoc out of the following line because there aren't enough tokens.\nLine: " + line);
             loc = genomeLocParser.createGenomeLoc(chr, Integer.valueOf(st.nextToken()), Integer.valueOf(st.nextToken()));
+        }
         return new AnnotatorInputTableFeature(loc.getContig(), (int)loc.getStart(), (int)loc.getStop());
     }