#!/usr/bin/python
import optparse
import sys
import os

from htsworkflow.util.opener import autoopen
from htsworkflow.util.makebed import make_bed_from_eland_stream, make_bed_from_multi_eland_stream, make_description

def make_parser():
  parser = optparse.OptionParser()
  parser.add_option('-e', '--eland', dest='inname',
                    help='specify input eland filename')
  parser.add_option('-b', '--bed', dest='outname',
                    help='specify output befilename')
  parser.add_option('-n', '--name', dest='name',
                    help='specify the track (short) name.',
                    default=None)
  parser.add_option('-d', '--description', dest='description',
                    help='specify the track description',
                    default=None)
  parser.add_option('--chromosome', dest='prefix',
                    help='Set the chromosome prefix name. defaults to "chr"',
                    default='chr')
  parser.add_option("--database", dest='database',
                    help="specify location of fctracker database",
                    default=None)
  parser.add_option("--flowcell", dest='flowcell',
                    help="compute name and description from database using flowcell id",
                    default=None)
  parser.add_option("--lane", dest='lane',
                    help='specify which lane to use when retrieving description from database',
                    default=None)

  multi = optparse.OptionGroup(parser, 'Multi-read ELAND support')

  multi.add_option('-m', '--multi', action='store_true',
                    help='Enable parsing multi-read eland files',
                    default=False)
  multi.add_option('--reads', type='int',
                   help='limit reporting multi reads to this many reads'
                        '(most usefully --reads=1 will turn a multi-read '
                        'file into a single read file)',
                   default=255)
  parser.add_option_group(multi)

  return parser

def main(command_line=None):
  instream = None
  outstream = None

  if command_line is None:
    command_line = sys.argv[1:]

  parser = make_parser()
  (options, args) = parser.parse_args(command_line)

  if options.inname is None:
    parser.error("Need eland input file name")
    return 1

  if options.inname == '-':
    instream = sys.stdin
  elif os.path.exists(options.inname):
    instream = autoopen(options.inname, 'r')
  else:
    parser.error('%s was not found' % (options.inname))
    return 1

  # figure out name for output file
  if options.outname is None:
      # if outname wasn't defined, and we're reading from stdout
      if instream is sys.stdin:
          # write to stdout
          outstream = sys.stdout
      else:
          # if there's a name write to name.bed
          options.outname = os.path.splitext(options.inname)[0]+'.bed'
          print >>sys.stderr, "defaulting to outputname", options.outname
  elif options.outname == '-':
      outstream = sys.stdout

  if outstream is None:
      if os.path.exists(options.outname):
          parser.error("not overwriting %s" % (options.outname))
          return 1
      else:
          outstream = open(options.outname, 'w')

  if options.flowcell is not None and options.lane is not None:
    # get our name/description out of the database
    name, description = make_description(
                           options.database, options.flowcell, options.lane
                        )
  else:
    name = options.name
    description = options.description

  if options.multi:
    make_bed_from_multi_eland_stream(instream, outstream, 
                                     name, description, 
                                     options.prefix,
                                     options.reads)

  else:
    make_bed_from_eland_stream(instream, outstream, 
                               name, description, 
                               options.prefix)
  return 0

if __name__ == "__main__":
  sys.exit(main(sys.argv[1:]))