# HG changeset patch
# User greg
# Date 1502458158 14400
# Node ID 7e22d880e551654d6db9702246487f4a477ba2e8
# Parent  a70690dcf9ffda435845bc97ff04746ed092c341
Uploaded

diff -r a70690dcf9ff -r 7e22d880e551 build_matrix.R
--- a/build_matrix.R	Fri Aug 11 09:11:40 2017 -0400
+++ b/build_matrix.R	Fri Aug 11 09:29:18 2017 -0400
@@ -12,9 +12,15 @@
 args <- parse_args(parser, positional_arguments=TRUE)
 opt <- args$options
 
-data_table <- read.table(opt$input)
-as.matrix(data_table)
-status <- match(data_table[,3], missing)
-data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="")
-data_table <- data_table[is.na(status)==TRUE,]
-write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE)
+#data_table <- read.table(opt$input)
+#as.matrix(data_table)
+#status <- match(data_table[,3], missing)
+#data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="")
+#data_table <- data_table[is.na(status)==TRUE,]
+#write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE)
+
+x=as.matrix(read.table(opt$input))
+t=match(x[,3],missing)
+x[,3]=paste(opt$work_dir, x[,1],".",x[,2],".bed.gz", sep="")
+x=x[is.na(t)==T,]
+write.table(array(x,dim=c(length(x)/3,3)), opt$output, quote=F,row.names=F,col.names=F)