# HG changeset patch
# User Ido Tamir <ido.tamir@imp.ac.at>
# Date 1376839096 -7200
# Node ID fcf85568a102d10f98a36f38a2862b1d69c5053e
# Parent  9abd178b46bd1822507ea7b889191026e6249231
dont know how this worked. added coverages to mappable

diff -r 9abd178b46bd -r fcf85568a102 corr.R
--- a/corr.R	Sun Aug 18 17:14:10 2013 +0200
+++ b/corr.R	Sun Aug 18 17:18:16 2013 +0200
@@ -124,8 +124,9 @@
    apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) })
 }
 
-getMappable <- function(mappable){
-    if(is.na(mappable)){
+getMappable <- function(coverages, mappable){
+    print(paste("creating mappability", mappable))
+	if(is.na(mappable)){
 	    createMappable(coverages)
     }else{
         import(mappable, format="bed", asRangedData = FALSE)
@@ -150,7 +151,7 @@
 
 
 coverages <- getCoverages(infiles, formats)
-mappability <- getMappable(mappable)
+mappability <- getMappable(coverages, mappable)
 
 calcAndPlot(coverages, outnames, mappability, outnamePDF, outnameMat,title)