From e0d091b3db19f2e56cdf6ba30e5f6b75dc11ee35 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 6 Jan 2011 15:39:08 +0000
Subject: [PATCH] Die gracefully if the bam is malformed with quals that are
 too high

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4952 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/genotyper/DiploidSNPGenotypeLikelihoods.java | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index 2835dea11..7fdb997d0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -26,15 +26,14 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
-import java.util.HashSet;
-import java.util.Set;
-
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
 
@@ -331,6 +330,8 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
                              SAMRecord read, DiploidSNPGenotypeLikelihoods val ) {
         int i = BaseUtils.simpleBaseToBaseIndex(observedBase);
         int j = qualityScore;
+        if ( j > SAMUtils.MAX_PHRED_SCORE )
+            throw new UserException.MalformedBam(read, String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s", SAMUtils.MAX_PHRED_SCORE, j, read.getReadName()));
         int k = ploidy;
         int x = strandIndex(! read.getReadNegativeStrandFlag() );
 
@@ -341,6 +342,8 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
                                             byte observedBase, byte qualityScore, int ploidy, SAMRecord read) {
         int i = BaseUtils.simpleBaseToBaseIndex(observedBase);
         int j = qualityScore;
+        if ( j > SAMUtils.MAX_PHRED_SCORE )
+            throw new UserException.MalformedBam(read, String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s", SAMUtils.MAX_PHRED_SCORE, j, read.getReadName()));
         int k = ploidy;
         int x = strandIndex(! read.getReadNegativeStrandFlag() );
         return cache[i][j][k][x];