def __init__(self, filename_or_sequence):
FileOrSequence.__init__(self, filename_or_sequence)
self.metadata = {}
self.info = {}
self.filters = {}
self.formats = {}
self.nsamples = 0
self.sampleids = []
def __init__(self, filename_or_sequence, verbose=True):
FileOrSequence.__init__(self, filename_or_sequence)
self.attributes = {}
self.stepType = 'none'
self.verbose = verbose
def __init__(self, file_, raw_iterator=False):
FileOrSequence.__init__(self, file_)
self.raw_iterator = raw_iterator
def __init__(self, filename_or_sequence, solexa_old=False):
FileOrSequence.__init__(self, filename_or_sequence)
if solexa_old:
self.qualscale = "solexa-old"
else:
self.qualscale = "solexa"
def __init__(self, file_, qual_scale="phred", raw_iterator=False):
FileOrSequence.__init__(self, file_)
self.qual_scale = qual_scale
if qual_scale not in ("phred", "solexa", "solexa-old"):
raise ValueError("Illegal quality scale.")
self.raw_iterator = raw_iterator
def __init__(self, filename_or_sequence):
FileOrSequence.__init__(self, filename_or_sequence)