def __init__(self, argumentList):
"""Initialize a PBAlign object.
argumentList is a list of arguments, such as:
['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
"""
desc = "Utilities for aligning PacBio reads to reference sequences."
super(PBAlign, self).__init__(desc)
self._argumentList = argumentList
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()
self.parser, self.args, _infoMsg = parseOptions(
argumentList=self._argumentList, parser=self.parser)
# args.verbosity is computed by counting # of 'v's in '-vv...'.
# However in parseOptions, arguments are parsed twice to import config
# options and then overwrite them with argumentList (e.g. command-line)
# options.
self.args.verbosity = 0 if (self.args.verbosity is None) else \
int(self.args.verbosity) / 2
