prepareData

#!/bin/bash

#Flags used
mapFlag=0;
gcFlag=0;
windowFlag=0;

SOURCEDIR=$(dirname $(readlink -f $0)); # SOURCE DIRECTORY

SHORTOPTS="o:m:g:"
LONGOPTS="win:,help,genome_file:"
PROGNAME="prepare_data.sh"
ARGS=$(getopt -s bash --options $SHORTOPTS  --longoptions $LONGOPTS --name $PROGNAME -- "$@" )

eval set -- "$ARGS"
while true; do
	case "$1" in
	-m) map_file="$2"; mapFlag=1; shift 2; ;;
        -g) gc_file="$2"; gcFlag=1; shift 2; ;;
        -o) output_file="$2"; shift 2;;
        --win) window_size="$2"; windowFlag=1; shift 2; ;;
	--genome_file) gen_file="$2"; genFlag=1; shift 2; ;;
        --help) echo "Usage: prepare_data -m <map file> -g <gc content file> --win <window_Size> --genome_file <Genome file> -o <output Prefix> ";
         exit 1; ;;
        --) shift; break;;
        *) echo "Error: Something wrong with the parameters";
	echo "Requred parameters: -i -o -m -z "; exit 1;;
	esac
done
# MINIMUM REQUIRED PARAMETERS
#if [[ -z "$map_file" || -z "$gc_file" || -z "$window_size" || -z "$gen_file"|| -z "$output" ]]; then
#	echo "Missing one of the required parameters: mappability_file (-m) gc_file (-g) window_size (--win) genome_file (--genome_file) or output (-o) " >&2
#	exit
#fi

# FILE DOESNT EXIST ERROR
if [[ ! -f $map_file || ! -f $gc_file || ! -f $gen_file ]]; then
	echo "One of the input files not found" >&2
      	exit 1
fi

#Generate Bin file
bedtools makewindows -w "$window_size" -g "$gen_file" > $output_file"_"$window_size".bin";

# Generate Map and GC files

Rscript --slave $SOURCEDIR"/source/R/generateMap.R" $map_file "$window_size" $(awk '{print $2}' $gen_file) $output_file; 
Rscript --slave $SOURCEDIR"/source/R/generateGC.R" $gc_file "$window_size" $(awk '{print $2}' $gen_file) $output_file;