# HG changeset patch
# User Ido Tamir <ido.tamir@imp.ac.at>
# Date 1379936784 -7200
# Node ID de452b96da8eb3907b9a8ad386c993ec23859a5c
# Parent  f3e037496c18b27d3a114ecc24ed588234bf8539
added bam input

diff -r f3e037496c18 -r de452b96da8e corr.R
--- a/corr.R	Sun Aug 18 21:33:43 2013 +0200
+++ b/corr.R	Mon Sep 23 13:46:24 2013 +0200
@@ -17,10 +17,13 @@
 
 options("useFancyQuotes" = FALSE)
 
+TEST=FALSE
+
 library(rtracklayer)
 library(lattice)
 library(latticeExtra)
 library(hexbin)
+library(Rsamtools)
 
 ## creates the union of coverages i.e. mappable regions
 ## todo: add mappability argument
@@ -109,7 +112,11 @@
 
 getCoverage <- function(infile, format){
   print(paste("reading", infile, format))
-  values <- import(infile, format=format, asRangedData = FALSE)  
+  values <- if(format == "bam"){
+     import(infile, format=format)
+  }else{
+     import(infile, format=format, asRangedData = FALSE)
+  } 
   if(tolower(format) %in% c("bigwig","wig")){
      values
   }else{
@@ -157,6 +164,17 @@
 
 args <- commandArgs(TRUE)
 
+if(TEST){
+  args[1] <- c("file1.bed,file2.bed,file3.bed,file4.bed")
+  args[1] <- c("file1.bam,file2.bam,file3.bam,file4.bam")
+  args[2] <- c("file1,file2,file3,file4")
+  args[3] <- c("bam,bam,bam,bam")
+  args[4] <- "out.pdf"
+  args[5] <- "mat.mat"
+  args[6] <- "title"
+  args[7] <- NA
+}
+
 infiles <- unlist(strsplit(args[1], ","))
 outnames <- unlist(strsplit(args[2], ","))
 formats <- unlist(strsplit(args[3], ","))
diff -r f3e037496c18 -r de452b96da8e corr.xml
--- a/corr.xml	Sun Aug 18 21:33:43 2013 +0200
+++ b/corr.xml	Mon Sep 23 13:46:24 2013 +0200
@@ -40,7 +40,7 @@
 Requirements:
 -------------
 
-At least two files of 6 column bed, wig(?) or bigWig format 
+At least two files of 6 column bed, wig, bam or bigWig format 
 
 Outputs:
 --------
@@ -52,7 +52,6 @@
 TODO:
 -----
 -    Add mappability track option
--    Add bam as input
    </help> 
 </tool>