From a8a2c1a2a19febdf9d49b1f4c71e2a4d32da2c41 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Oct 2009 01:19:58 +0000
Subject: [PATCH] Replaced SSG with UG in packaging utils.  Minor performance
 and formatting improvements for ClipReads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/ClipReadsWalker.java | 10 ++++------
 packages/GenomeAnalysisTK.xml                          |  2 +-
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java
index a4f281d9d..fb3f18adf 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java
@@ -59,9 +59,6 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
     @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
     String outputBamFile = null;
 
-    @Argument(fullName = "", shortName = "STD", doc = "FOR DEBUGGING ONLY", required = false)
-    boolean toStandardOut = false;
-
     @Argument(fullName = "qTrimmingThreshold", shortName = "QT", doc = "", required = false)
     int qTrimmingThreshold = -1;
 
@@ -304,9 +301,10 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
     public ClippingData reduceInit() {
         SAMFileWriter outputBam = null;
 
-        if ( outputBamFile != null && ! toStandardOut ) {
+        if ( outputBamFile != null ) {
             SAMFileHeader header = this.getToolkit().getSAMFileHeader();
-            outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, 5);
+            boolean maintainsSort = clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES;
+            outputBam = Utils.createSAMFileWriterWithCompression(header, maintainsSort, outputBamFile, 5);
         }
 
         return new ClippingData(outputBam, sequencesToClip);
@@ -315,7 +313,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
     public ClippingData reduce(ReadClipper clipper, ClippingData data) {
         if (data.output != null) {
             data.output.addAlignment(clipper.clipRead(clippingRepresentation));
-        } else if (toStandardOut) {
+        } else {
             out.println(clipper.clipRead(clippingRepresentation).format());
         }
 
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 43002aa3f..0ece47fa6 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -24,7 +24,7 @@
     <!-- Variant filtration -->
     <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
     <!-- Single sample genotyper -->
-    <class>org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper</class>
+    <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
     <!-- And the filters -->
     <class>org.broadinstitute.sting.gatk.walkers.filters.IVFSecondaryBases</class>
     <class>org.broadinstitute.sting.gatk.walkers.filters.VECFisherStrand</class>