From 5cf4fd63c25ba7714418cae4579d56398b498556 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 8 May 2012 09:34:57 -0400
Subject: [PATCH] Catch malformed base qualities and throw as a User Error

---
 .../walkers/recalibration/TableRecalibrationWalker.java     | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 08151321f..8eaa0198a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -425,7 +425,11 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         read.setBaseQualities(recalQuals); // Overwrite old qualities with new recalibrated qualities
         if (!DO_NOT_WRITE_OQ && read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null) { // Save the old qualities if the tag isn't already taken in the read
-            read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
+            try {
+                read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
+            } catch (IllegalArgumentException e) {
+                throw  new UserException.MalformedBAM(read, "illegal base quality encountered; " + e.getMessage());
+            }
         }
 
         if (!skipUQUpdate && refBases != null && read.getAttribute(SAMTag.UQ.name()) != null) {