From 6f56938d428611c1e960a19b648941824a8197d7 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Apr 2009 15:20:26 +0000
Subject: [PATCH] * added a bit more debugging output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/SomaticCoverageWalker.java     | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
index 499843a08..72a8343cc 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
@@ -62,6 +62,7 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
         List<SAMRecord> reads = context.getReads();
         int tumorDepth = 0;
         int normalDepth = 0;
+        StringBuilder readNames = new StringBuilder();
         for ( int i = 0; i < reads.size(); i++ )
         {
             SAMRecord read = reads.get(i);
@@ -98,6 +99,7 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
             } else {
                 throw new RuntimeException("Unknown Sample Name: " + sample);
             }
+            readNames.append(read.getReadName()).append("+").append(read.getAlignmentStart()).append("+").append(read.getCigarString());
 
         }
 
@@ -129,9 +131,12 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
         }
         lastPosition = context.getPosition();
 
+        if (extendedOutput) {
+            sb.append(context.getPosition()).append(" ");
+        }
         sb.append((isTumorCovered && isNormalCovered)?"1":"0");
         if (extendedOutput) {
-            sb.append(" ").append(tumorDepth).append(" ").append(normalDepth);
+            sb.append(" ").append(tumorDepth).append(" ").append(normalDepth).append(" ").append(readNames);
         }
 
 //        sb.append(context.getContig()).append(" ");