From 9ab647b7300bbe043c4af709048e5664da1c5227 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 16 Aug 2010 13:34:32 +0000
Subject: [PATCH] adding checks to the RefSeq rod for line's that contain less
 than the required number of columns (we expect there to be 16 columns)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4041 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/features/refseq/RefSeqCodec.java      | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
index 2cf26f70b..122fd876d 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
@@ -2,11 +2,13 @@ package org.broadinstitute.sting.gatk.refdata.features.refseq;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -18,6 +20,7 @@ public class RefSeqCodec implements FeatureCodec {
     @Override
     public Feature decodeLoc(String line) {
         String fields[] = line.split("\t");
+        if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
         String contig_name = fields[2];
         return new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
     }
@@ -27,6 +30,8 @@ public class RefSeqCodec implements FeatureCodec {
     public Feature decode(String line) {
         String fields[] = line.split("\t");
 
+        // we reference postion 15 in the split array below, make sure we have at least that many columns
+        if (fields.length < 16) throw new TribbleException("RefSeq (decode) : Unable to parse line -> " + line + ", we expected at least 16 columns, we saw " + fields.length);
         String contig_name = fields[2];
         RefSeqFeature feature = new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));