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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
This commit is contained in:
corin 2011-02-03 18:32:05 +00:00
parent b1ff371c8f
commit 9fc45e1234
1 changed files with 2 additions and 2 deletions
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4
R/DataProcessingReport/GetTearsheetStats.R
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@ -16,7 +16,7 @@ suppressMessages(library(ROracle));
cmdargs = gsa.getargs( cmdargs = gsa.getargs(
list( 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"), bamlist = list(value=NA, doc="list of BAM files"),
evalroot = list(value=NA, doc="VariantEval root"), evalroot = list(value=NA, doc="VariantEval root"),
tearout = list(value=NA, doc="Output path for tearsheet PDF")#, tearout = list(value=NA, doc="Output path for tearsheet PDF")#,
@ -28,7 +28,7 @@ cmdargs = gsa.getargs(
bamlist = scan(cmdargs$bamlist, "character"); bamlist = scan(cmdargs$bamlist, "character");
#print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep="")) #print(paste("grep SQUID ", cmdargs$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(); indexed = c();
nonindexed = c(); nonindexed = c();
for (bam in bamlist) { for (bam in bamlist) {