#! /bin/bash

while getopts "m:k:" optkey; do
        case $optkey in
	     m) mapper=$OPTARG;;
	     k) kmer=$OPTARG;;
        esac
done
shift $((OPTIND-1))

if [ $# -lt 1 ]; then
	echo "usage: imrdenom <project_description_file>"
	exit
fi
Bin="$( readlink -f -- "${0%/*}" )"
des=$1

echo "running IMR"
strmapper=""
if [ "$mapper" ]; then
	strmapper=" -m $mapper "   
fi
$Bin/imr easyrun $strmapper $des

echo "running DENOM"
strkmer=""
if [ "$kmer" ]; then
	strkmer=" -k $kmer " 
fi
$Bin/denom soapinterface $strkmer $des



echo "running MCMERGE"
$Bin/mcmerge configrun $des
