From bd53bc18f92aab50cbd2ecaab642a00339d5fc62 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 17 May 2009 12:24:06 +0000
Subject: [PATCH] added new required annotations

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/SomaticMutationWalker.java | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
index 01b0311b5..e00139c68 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
@@ -6,6 +6,8 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.By;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
 import net.sf.samtools.SAMRecord;
@@ -14,6 +16,7 @@ import java.util.List;
 import java.util.HashMap;
 import java.util.Map;
 
+@By(DataSource.REFERENCE)
 public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
     protected static class QualitySums {
         private int a = 0;
@@ -73,6 +76,8 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
     public static int MIN_MUTANT_SUM_PRETEST = 60;
     public static int MIN_MUTANT_SUM = 100;
 
+    public static int MIN_QSCORE = 13;
+
     public static double TUMOR_LOD = 6.3d;
 //    public static double TUMOR_LOD = 1.0d;
     public static double NORMAL_LOD = 2.3d;
@@ -138,11 +143,11 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
             
             if (normalSampleName.equals(sample)) {
                 normalGL.add(ref, base, qual);
-                normalQualitySums.incrementSum(base, qual);
+                if (qual > MIN_QSCORE) normalQualitySums.incrementSum(base, qual);
                 normalBases.append(base);
             } else if (tumorSampleName.equals(sample)) {
                 tumorGL.add(ref, base, qual);
-                tumorQualitySums.incrementSum(base, qual);
+                if (qual > MIN_QSCORE) tumorQualitySums.incrementSum(base, qual);
                 tumorBases.append(base);
 
                 int midDist = Math.abs((int)(read.getReadLength() / 2) - offset);
@@ -204,6 +209,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                         "__NScore:" + normalLod +
                         "__NRefSum: " + normalQualitySums.get(ref) +
                         "__NAltSum: " + normalQualitySums.get(altAllele) +
+                        "__MIDP: " + midp.get(altAllele) + 
                         (failedMidpointCheck?"__FAILED-MPCHECK":"")
                 );