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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
This commit is contained in:
corin 2011-02-01 15:47:52 +00:00
parent 91297c138b
commit 027c91871f
1 changed files with 3 additions and 3 deletions
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6
R/DataProcessingReport/GetTearsheetStats.R
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@ -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) {