From d1b525b4287c950b92cfbd59c0d7d2375dea795c Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Nov 2009 19:24:27 +0000
Subject: [PATCH] Default window size for NQS covariate is 3

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2040 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/Recalibration/CovariateCounterWalker.java      | 2 +-
 .../gatk/walkers/Recalibration/TableRecalibrationWalker.java    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
index fb7274604..55990542c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
@@ -71,7 +71,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     @Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
     private String PLATFORM = "SLX";
     @Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
-    private int WINDOW_SIZE = 1;
+    private int WINDOW_SIZE = 3;
     @Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file")
     private String RECAL_FILE = "output.recal_data.csv";
     @Argument(fullName="noPrintHeader", shortName="noHeader", required=false, doc="Don't print the usual header on the table recalibration file")
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
index fd8a5b13c..caf129cc7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java
@@ -67,7 +67,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     @Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
     private String PLATFORM = "SLX";
     @Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
-    private int WINDOW_SIZE = 1;
+    private int WINDOW_SIZE = 3;
     @Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points")
     public int SMOOTHING = 1;