From 338cdbebad769ed154419083c776ccdb97639586 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 5 Jul 2009 16:49:58 +0000
Subject: [PATCH] deal with screwy solid reads in the cleaner (no cigar
 strings)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1171 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/indels/IntervalCleanerWalker.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
index c0f9b1746..5e34544e8 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -225,8 +225,8 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         // decide which reads potentially need to be cleaned
         for ( SAMRecord read : reads ) {
 
-            // we currently can not deal with clipped reads correctly
-            if ( readIsClipped(read) ) {
+            // we currently can not deal with clipped reads correctly (or screwy record)
+            if ( read.getCigar().numCigarElements() == 0 || readIsClipped(read) ) {
                 refReads.add(read);
                 continue;
             }