#!/usr/bin/env ruby

require 'optparse'
require 'bio-logger'

SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')

# Parse command line options into the options hash
options = {
  :logger => 'stderr',
  :log_level => 'info',
}
o = OptionParser.new do |opts|
  opts.banner = "
    Usage: #{SCRIPT_NAME} <arguments>

    Description of what this program does...\n\n"

  opts.on("--velvet-pregraph GRAPH_FILE", "PreGraph file output from velveth [required]") do |arg|
    options[:velvet_pregraph_file] = arg
  end

  # logger options
  opts.separator "\nVerbosity:\n\n"
  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
end; o.parse!
if ARGV.length != 0 or options[:velvet_pregraph_file].nil?
  $stderr.puts o
  exit 1
end
# Setup logging
Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)


# Read in the velvet graph
log.info "Parsing graph from #{options[:velvet_pregraph_file]}"
graph = Bio::Velvet::Graph.parse_from_file(options[:velvet_pregraph_file])
log.info "Finished parsing graph, found #{graph.number_of_nodes} nodes"

# Log the number of nodes and arcs in the current graph

# Read in the fasta file of immutable nodes, and extract the two most immutable
# Log that they are found

# Determine that the graph is connected or not between the two most immutable nodes, using some graph theoretic algorithm
# If the graph is not connected, then there is no hope, exit

# Go through the graph to get a list of the cap nodes
# Log the number of cap nodes found

# Trim off all the cap nodes back to cross nodes, keeping track of the lengths

# Print the graph in graphviz dot format