diff QDNAseq.R @ 30:647143d0c884 draft

Uploaded

--- a/QDNAseq.R	Wed Jun 18 05:33:04 2014 -0400
+++ b/QDNAseq.R	Wed Jun 18 05:45:02 2014 -0400
@@ -116,10 +116,8 @@
 
 	sampleCount <- length( regionsList )
 	sampleNames <- names( regionsList )
-	systemUser <- system("whoami",T)
 	bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )
-
-	cat( MAIN_NAME, " Hello ", systemUser, "!!\n", sep="")
+	
 	cat( MAIN_NAME, " There are ", sampleCount, " samples found in input list...\n", sep="")
 
 	for ( sample in sampleNames ){		
@@ -179,14 +177,17 @@
 DECIMALS  <- 3
 WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
 
+
+
 catMsg( "Starting QDNAseq wrapper" )	
 catMsg( "Loading R libraries" )
 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
 
+systemUser <- system("whoami",T)
 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
-qdnaseqDate <- packageDescription( "QDNAseq" )$Date
-catMsg( paste("QDNAseq info: version(", qdnaseqVersion, ") and date (", qdnaseqDate, ")", sep="") )
+catMsg( c(" Hello ", systemUser ) )
+catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) )
 
 ## only one param: the tmp config file
 cmdLineArgs <- commandArgs(TRUE)
@@ -350,13 +351,9 @@
 		plotted_images[[ sample ]][[ 'region_count' ]] <- region_count
 	}
 
-	## add read counts
-	catMsg( "Used")
-	catMsg( usedReads )
-
+	## add USED read counts
 	plotted_images[[ sample ]][[ 'usedReads'  ]] <- usedReads
 }
-#cat( MAIN_NAME, "PLOTTED_IMAGES: ", names(plotted_images), "\n", sep="" )
 
 if ( doCall ){
 	saveRDS( regions, robjRegionPath )