From 01e032e89c360d24ff8296fa260b36c3bc6f5913 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 26 Jan 2011 14:09:39 +0000
Subject: [PATCH] Missorted BAMs are User Exceptions

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5080 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/VerifyingSamIterator.java            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
index 2499f1e9a..13c381161 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.util.RuntimeIOException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Iterator;
 
@@ -35,7 +35,7 @@ public class VerifyingSamIterator implements StingSAMIterator {
     private void verifyRecord( final SAMRecord last, final SAMRecord cur ) {
         if ( checkOrderP && isOutOfOrder(last, cur) ) {
             this.last = null;
-            throw new RuntimeIOException(String.format("Reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()) );
+            throw new UserException.MissortedBAM(String.format("reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()) );
         }
     }