From efceb0d48c4ee466ad762c53e8fe3e54b4823fdc Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 26 Dec 2012 14:30:51 -0500
Subject: [PATCH] Check for well-encoded reads while fixing mis-encoded ones

---
 .../sting/utils/sam/MisencodedBaseQualityReadTransformer.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
index cac51239a..17d40e530 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
@@ -47,6 +47,8 @@ public class MisencodedBaseQualityReadTransformer extends ReadTransformer {
         final byte[] quals = read.getBaseQualities();
         for ( int i = 0; i < quals.length; i++ ) {
             quals[i] -= encodingFixValue;
+            if ( quals[i] < 0 )
+                throw new UserException.BadInput("while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool");
         }
         read.setBaseQualities(quals);
         return read;