From 9fc45e12348ca60d1b28d37a210a5dfda93e1146 Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Feb 2011 18:32:05 +0000
Subject: [PATCH] Use the yaml as an arguemtn to get out squid numbers

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5186 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/DataProcessingReport/GetTearsheetStats.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/DataProcessingReport/GetTearsheetStats.R b/R/DataProcessingReport/GetTearsheetStats.R
index 54f9b24bd..e7ac7a436 100644
--- a/R/DataProcessingReport/GetTearsheetStats.R
+++ b/R/DataProcessingReport/GetTearsheetStats.R
@@ -16,7 +16,7 @@ suppressMessages(library(ROracle));
 
 cmdargs = gsa.getargs(
     list(
-        #yaml = list(value=NA, doc="pipeline YAML file"),
+        yaml = list(value=NA, doc="pipeline YAML file"),
         bamlist = list(value=NA, doc="list of BAM files"),
         evalroot = list(value=NA, doc="VariantEval root"),
         tearout = list(value=NA, doc="Output path for tearsheet PDF")#,
@@ -28,7 +28,7 @@ cmdargs = gsa.getargs(
 
 bamlist = scan(cmdargs$bamlist, "character");
 #print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o',  sep=""))
-squids <- system(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist), ' |grep "C..." -o',  sep=""), intern=TRUE)
+squids <- system(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o',  sep=""), intern=TRUE)
 indexed = c();
 nonindexed = c();
 for (bam in bamlist) {