From 027c91871f475fa8c44e3940882c9c358ea99f46 Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Feb 2011 15:47:52 +0000
Subject: [PATCH] Commenting out something I meant to leave commented out

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5163 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/DataProcessingReport/GetTearsheetStats.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/DataProcessingReport/GetTearsheetStats.R b/R/DataProcessingReport/GetTearsheetStats.R
index daab5c74e..54f9b24bd 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")#,
@@ -27,8 +27,8 @@ cmdargs = gsa.getargs(
 
 
 bamlist = scan(cmdargs$bamlist, "character");
-print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o',  sep=""))
-squids <- system(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o',  sep=""), intern=TRUE)
+#print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o',  sep=""))
+squids <- system(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist), ' |grep "C..." -o',  sep=""), intern=TRUE)
 indexed = c();
 nonindexed = c();
 for (bam in bamlist) {