From a975db2c2e2fa8a5c33965fe9d7e0c4a319d93b6 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Sep 2010 16:58:54 +0000
Subject: [PATCH] Bug fix for the case of reads with no read bases!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4184 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/TableRecalibrationWalker.java  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index dde60fc5f..ebf18aa90 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -334,6 +334,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      */
     public SAMRecord map( ReferenceContext refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker  ) {
 
+        if( read.getReadLength() == 0 ) { // Some reads have '*' as the SEQ field and samtools returns length zero. We don't touch these reads.
+            return read;
+        }
+
         RecalDataManager.parseSAMRecord( read, RAC );
 
         byte[] originalQuals = read.getBaseQualities();