From a343f3eab74afb94212e8f4423c068397fa74f30 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 27 Apr 2009 15:17:20 +0000
Subject: [PATCH] Fixed bug where we weren't setting the reads group correctly.
  Also added code to set the printMetrics field of the singleSampleGenotyper
 from the Pool caller, it was null excepting out for me without that set.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@548 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../iterators/MergingSamRecordIterator2.java  |  5 ++++-
 .../playground/gatk/walkers/PoolCaller.java   | 22 ++++++++++---------
 2 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 44145f562..693ba08c5 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -138,7 +138,10 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         if (oldProgramGroupId != null) {
             final String newProgramGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldProgramGroupId);
             record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
-        } else {
+        }
+
+        // if we don't have a read group, set one correctly
+        if (record.getAttribute(SAMTag.RG.toString()) == null) {
             List<SAMReadGroupRecord> readGroups = iterator.getReader().getFileHeader().getReadGroups();
             if (readGroups.size() == 1) {
                 record.setAttribute(SAMTag.RG.toString(), readGroups.get(0).getReadGroupId());
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
index 1815866f3..656648342 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
@@ -1,21 +1,22 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
+import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
 
 public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String> 
 {
@@ -56,6 +57,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
             caller.metricsFileName = "/dev/null";
             caller.lodThreshold = 5.0;
             caller.fourBaseMode = false;
+            caller.printMetrics = false;
             caller.initialize();
             callers.add(caller);
         }