From 98798eb2761988d684ad4694b75db23366935c68 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 2 Apr 2011 22:28:41 +0000
Subject: [PATCH] Adding ReadPos rank sum test.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5560 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/annotator/ReadPosRankSumTest.java | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
new file mode 100755
index 000000000..e67061e48
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -0,0 +1,41 @@
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: rpoplin
+ * Date: 3/30/11
+ */
+
+public class ReadPosRankSumTest extends RankSumTest {
+
+    public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }
+
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias")); }
+
+    protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
+        for ( final PileupElement p : pileup ) {
+            if( isUsableBase(p) ) {
+                int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p.getOffset(), 0, 0);
+                final int numAlignedBases = AlignmentUtils.getNumAlignedBases(p.getRead());
+                if( readPos > numAlignedBases / 2 ) {
+                    readPos = numAlignedBases - ( readPos + 1 );
+                }
+
+                if ( p.getBase() == ref ) {
+                    refQuals.add( readPos );
+                } else if ( p.getBase() == alt ) {
+                    altQuals.add( readPos );
+                }
+            }
+        }
+    }
+}