From bb666ce392ae13ee80f050525cbea50568214123 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Apr 2009 00:51:26 +0000
Subject: [PATCH] Added mappingQualPileup function for use in the verbose mode
 of Pileup

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/Utils.java | 10 ++++++++++
 1 file changed, 10 insertions(+)

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<Byte> mappingQualPileup( List<SAMRecord> reads) {
+        ArrayList<Byte> 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<SAMRecord> reads, List<Integer> offsets ) {
         StringBuilder quals = new StringBuilder();
         for ( int qual : qualPileup(reads, offsets)) {