compatible with GATK 2.7.1 (includes bugfix for MAPQ > 127 causing ov…

…erflows in MuTect)
broadinstitute · Aug 22, 2013 · 8f5ae96 · 8f5ae96
1 parent f07a1d1
commit 8f5ae96
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java b/src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java
@@ -575,10 +575,10 @@ public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref,
                 final LocusReadPile refPile =  new LocusReadPile(referencePileup, altAllele, 0, 0, MTAC.ENABLE_QSCORE_OUTPUT);
 
                 // Set the maximum observed mapping quality score for the reference and alternate alleles
-                byte[] rmq = referencePileup.getMappingQuals();
+                int[] rmq = referencePileup.getMappingQuals();
                 candidate.setTumorRefMaxMapQ((rmq.length==0)?0:NumberUtils.max(rmq));
 
-                byte[] amq = mutantPileup.getMappingQuals();
+                int[] amq = mutantPileup.getMappingQuals();
                 candidate.setTumorAltMaxMapQ((amq.length==0)?0:NumberUtils.max(amq));
 
                 candidate.setStrandContingencyTable(SequenceUtils.getStrandContingencyTable(refPile, mutantPile));