From 58f7b4c5956d88980685dd041c3f5167218b500c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 29 Oct 2010 14:41:38 +0000
Subject: [PATCH] Naughty use of assertions means that malformed records are
 not caught.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4596 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/features/refseq/RefSeqCodec.java   | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

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 f46d41b9a..d8a5a479e 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
@@ -38,7 +38,7 @@ public class RefSeqCodec implements FeatureCodec {
         feature.setTranscript_id(fields[1]);
         if ( fields[3].length()==1 && fields[3].charAt(0)=='+') feature.setStrand(1);
         else if ( fields[3].length()==1 && fields[3].charAt(0)=='-') feature.setStrand(-1);
-        else throw new UserException.MalformedFile("Expected strand symbol (+/-), found: "+fields[3]);
+        else throw new UserException.MalformedFile("Expected strand symbol (+/-), found: "+fields[3] + " for line=" + line);
 
 
         feature.setTranscript_interval(GenomeLocParser.parseGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));
@@ -48,8 +48,10 @@ public class RefSeqCodec implements FeatureCodec {
         String[] exon_stops = fields[10].split(",");
         String[] eframes = fields[15].split(",");
 
-        assert exon_starts.length == exon_stops.length : "Data format error: numbers of exon start and stop positions differ";
-        assert exon_starts.length == eframes.length : "Data format error: numbers of exons and exon frameshifts differ";
+        if ( exon_starts.length == exon_stops.length )
+            throw new UserException.MalformedFile("Data format error: numbers of exon start and stop positions differ for line=" + line);
+        if ( exon_starts.length == eframes.length )
+            throw new UserException.MalformedFile("Data format error: numbers of exons and exon frameshifts differ for line=" + line);
 
         ArrayList<GenomeLoc> exons = new ArrayList<GenomeLoc>(exon_starts.length);
         ArrayList<Integer> exon_frames = new ArrayList<Integer>(eframes.length);