##
## Read raw data from UCSC download site.  For each, create interpolated and
## non-interpolated bed files, one for each ENCODE region.
## 
## Run with
##
##  $ R --no-save < runall.score.R
##
## Author:  RET
## Date:    11/17/05
## Project: encode-chrom
##

## Definitions of some functions we'll need.
source("../../../../bin/bed.R")

############################################
##
## Parameters
##
############################################
project <- 'UvaDnaRepTr50'
method <- 'tb'

bedloc <- paste("../../bed/", project, sep = "")
comfybedloc <- paste("../../comfy-bed/", project, sep = "")
## Target resolution (>= 50bp).
res <- 50

## The original data track tables to be downloaded from UCSC.
## See Table Browser (may need to view source for the "get output" button
## for appropriate names).
tb.track <- paste('encode', project, sep = '')
files <- tb.track
## The tissue for each table
tissues <- 'HeLa'
## The experiment for each table.
experiments <- ''

## gap-filling method
gap.method <- 'adapt.loess'
gap <- 2000
loess.degree <- 1
loess.window <- 50

## Make it so.
UCSC2bed(project, files = files, bedloc = bedloc, comfybedloc = comfybedloc,
         res = res, method = method, tissues = tissues,
         experiments = experiments, tb.track = tb.track,
         gap = gap, loess.degree = loess.degree,
         loess.window = loess.window, check = F)