From 6db3e473af175328166cf5aea9e0bd94ff9a9e31 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 17 Jan 2013 10:30:04 -0500
Subject: [PATCH] Better error message for bad qual

---
 .../gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index fc7573f21..8c8de2bad 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -425,7 +425,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
         byte qual = p.getQual();
 
         if ( qual > SAMUtils.MAX_PHRED_SCORE )
-            throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s.  Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
+            throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")");
         if ( capBaseQualsAtMappingQual )
             qual = (byte)Math.min((int)qual, p.getMappingQual());
         if ( (int)qual < minBaseQual )