From f4ffef447928983c1ccaf555a18f84f996fb5079 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 7 Aug 2010 13:58:32 +0000
Subject: [PATCH] Default max variants is now 5000

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3966 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/VariantRecalibratorReport/VariantRecalibratorReport.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/VariantRecalibratorReport/VariantRecalibratorReport.R b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
index 6dc2cb51c..8907106dd 100644
--- a/R/VariantRecalibratorReport/VariantRecalibratorReport.R
+++ b/R/VariantRecalibratorReport/VariantRecalibratorReport.R
@@ -17,7 +17,7 @@ lociFile = args[4];
 if (is.na(lociFile) | lociFile == "NA" ) { lociFile = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.loci"; }
 
 maxVariants = args[5];
-if (is.na(maxVariants)) { maxVariants = -1; }
+if (is.na(maxVariants)) { maxVariants = 5000; }
 maxVariants = as.integer(maxVariants)
 
 greedy = args[6]