diff filter.R @ 5:b7f3854e08f8

Adding all tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.R	Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,25 @@
+args<-commandArgs(TRUE)
+
+input=args[1]
+length=as.numeric(args[2])
+probes=as.numeric(args[3])
+tmp_dir=args[4]
+nbcall=as.vector(args[5])
+output=args[6]
+
+nbcall_tmp <- strsplit(nbcall,",")
+nbcall_vecstring <-unlist(nbcall_tmp)
+
+nbcall_vecstring
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics")
+setwd(workdir)
+
+segcall = read.table(input, header = TRUE)
+filtercall=filterSeg(segcall,length,probes,nbcall_vecstring)
+sink(output)
+print(format(filtercall),row.names=FALSE)
+sink()
+#write.table(filtercall,output,row.names = FALSE, quote = FALSE, sep = "\t")
+