#!/usr/bin/ruby
require 'logger'
require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics"
c = Bioinformatics.program 'Flash'
c.logger(Logger.new(STDOUT))
c.sequence1 = ARGV[0]
c.sequence2 = ARGV[1]
c.readLen = ARGV[2]
c.fragLen = ARGV[3]
c.maxOverlap = ARGV[4]
c.workPath = '/tmp/'
c.execute(c.lineCommand)

Kernel.system("cp #{c.outExtended} #{ARGV[5]}")
Kernel.system("cp #{c.outNotComb1} #{ARGV[6]}")
Kernel.system("cp #{c.outNotComb2} #{ARGV[7]}")