From ab1c48745beca74be9382e4b2dc3793488278d41 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 21 Mar 2012 12:13:52 -0400
Subject: [PATCH] Need to catch RuntimeExceptions coming out of Picard too so
 that they show up as UserErrors (some BAM errors are thrown as REs).

---
 .../gatk/iterators/MalformedBAMErrorReformatingIterator.java | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
index f5dee4961..ca155a27f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
@@ -6,6 +6,7 @@ import net.sf.samtools.util.CloseableIterator;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Iterator;
 
 /**
@@ -23,7 +24,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
     public boolean hasNext() {
         try {
             return this.it.hasNext();
-        } catch ( SAMFormatException e ) {
+        } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFileExceptions) sometimes
             throw new UserException.MalformedBAM(source, e.getMessage());
         }
     }
@@ -31,7 +32,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
     public SAMRecord next() {
         try {
             return it.next();
-        } catch ( SAMFormatException e ) {
+        } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFileExceptions) sometimes
             throw new UserException.MalformedBAM(source, e.getMessage());
         }
     }