#!/usr/bin/env ruby
=begin
-------------------------------------------------------------------
  ringreads.rb
-------------------------------------------------------------------
  started on 07MAR2020
-------------------------------------------------------------------
  all rights reserved to TOQUE
-------------------------------------------------------------------
  This Ruby script accepts a FASTA file of a circular reference DNA
  sequence and generates hypothetical Illumina reads with a given
  length of pair-mate reads separated with a given insertion length.
-------------------------------------------------------------------
=end

require "./ref"

if ARGV.size < 5 then
  puts
  puts "----------------------------------------------------------"
  puts " Usage: ./ringreads.rb reference rs rlen ilen cov imr dmr"
  puts "----------------------------------------------------------"
  puts "  reference: FASTA file of a reference sequence"
  puts "    rs: random seed"
  puts "  rlen: read length"
  puts "  slen: insert length"
  puts "   cov: coverage"
  puts "   imr: insertion mutation rate (optional)"
  puts "   dmr: deletion mutation rate (optional)"
  puts "----------------------------------------------------------"
  exit(1)
  puts
end

def Coverage 
 
end


# 2. Parameters
#
refname = ARGV.shift
rs = ARGV.shift.to_i
rlen = ARGV.shift.to_i
ilen = ARGV.shift.to_i
cov = ARGV.shift.to_i
if ARGV.size > 0 then
  imr = ARGV.shift.to_f
  dmr = ARGV.shift.to_f
end

# 3. Main Routine
#
# 3.1. Modify the refernece as a character array
#
ref = Ref.new(refname, rs, rlen, ilen, cov)
ref.makeReads
ref.writeReads