diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java index 2eb55b4a3..5a667df67 100755 --- a/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/java/src/org/broadinstitute/sting/utils/Utils.java @@ -148,6 +148,16 @@ public class Utils { return quals; } + public static ArrayList mappingQualPileup( List reads) { + ArrayList quals = new ArrayList(reads.size()); + for ( int i = 0; i < reads.size(); i++ ) { + SAMRecord read = reads.get(i); + byte qual = (byte)read.getMappingQuality(); + quals.add(qual); + } + return quals; + } + public static String qualPileupAsString( List reads, List offsets ) { StringBuilder quals = new StringBuilder(); for ( int qual : qualPileup(reads, offsets)) {