def count(self, bam, library_type, coverage=False, uniq_only=False, fpkm=False, norm='', multiple='complete', whitelist=None, blacklist=None, out=sys.stdout, quiet=False, start_only=False):
self.stranded = library_type in ['FR', 'RF']
self.chrom_lens = []
for chrom, chrom_len in zip(bam.references, bam.lengths):
self.chrom_lens.append((chrom, chrom_len))
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm, multiple, whitelist, blacklist, out, quiet, start_only)
def count(self, bam, library_type, coverage=False, uniq_only=False, fpkm=False, norm='', multiple='complete', whitelist=None, blacklist=None, out=sys.stdout, quiet=False, start_only=False):
self.uniq_only = uniq_only
self.multiple = multiple
self.whitelist = whitelist
self.blacklist = blacklist
self.library_type = library_type
self.stranded = library_type in ['FR', 'RF']
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm, multiple, whitelist, blacklist, out, quiet, start_only)
def count(self,
bam,
library_type,
coverage=False,
uniq_only=False,
fpkm=False,
norm='',
multiple='complete',
whitelist=None,
blacklist=None,
out=sys.stdout,
quiet=False,
start_only=False):
self.stranded = library_type in ['FR', 'RF']
self.chrom_lens = []
for chrom, chrom_len in zip(bam.references, bam.lengths):
self.chrom_lens.append((chrom, chrom_len))
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm,
multiple, whitelist, blacklist, out, quiet, start_only)
def count(self,
bam,
library_type,
coverage=False,
uniq_only=False,
fpkm=False,
norm='',
multiple='complete',
whitelist=None,
blacklist=None,
out=sys.stdout,
quiet=False,
start_only=False):
self.uniq_only = uniq_only
self.multiple = multiple
self.whitelist = whitelist
self.blacklist = blacklist
self.library_type = library_type
self.stranded = library_type in ['FR', 'RF']
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm,
multiple, whitelist, blacklist, out, quiet, start_only)
