From 1b1ec7e52dba6c838added2e32ff6c226e7bd15e Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Sep 2010 21:28:36 +0000
Subject: [PATCH] Changed default phasing window size to 10

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4235 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/ReadBackedPhasingWalker.java      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
index 0b3a98c68..22f74199e 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
@@ -67,8 +67,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     @Argument(fullName = "cacheWindowSize", shortName = "cacheWindow", doc = "The window size (in bases) to cache variant sites and their reads; [default:20000]", required = false)
     protected Integer cacheWindow = 20000;
 
-    @Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm; [default:20]", required = false)
-    protected Integer maxPhaseSites = 20; // 2^20 == 10^6 biallelic haplotypes
+    @Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm; [default:10]", required = false)
+    protected Integer maxPhaseSites = 10; // 2^10 == 10^3 biallelic haplotypes
 
     @Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing; [default:10.0]", required = false)
     protected Double phaseQualityThresh = 10.0; // PQ = 10.0 <=> P(error) = 10^(-10/10) = 0.1, P(correct) = 0.9