def v_cigar(self):
cigar = []
if self.removed_prefix:
cigar.extend((len(self.removed_prefix), 'S'))
if self.seq_start:
cigar.extend((self.seq_start, 'N'))
end = self.seq_start + self.pre_cdr3_length + self.num_gaps
ref = self.germline[self.seq_start:end]
qry = self.sequence[self.seq_start:end]
cigar.extend(funcs.get_cigar(ref, qry))
return ''.join([str(s) for s in cigar])
def v_cigar(self):
cigar = []
if self.removed_prefix:
cigar.extend((len(self.removed_prefix), 'S'))
if self.seq_start:
cigar.extend((self.seq_start, 'N'))
end = self.seq_start + self.pre_cdr3_length + self.num_gaps
ref = self.germline[self.seq_start:end]
qry = self.sequence[self.seq_start:end]
cigar.extend(funcs.get_cigar(ref, qry))
return ''.join([str(s) for s in cigar])
def j_cigar(self):
return ''.join(
funcs.get_cigar(self.germline[-self.post_cdr3_length:],
self.sequence[-self.post_cdr3_length:]))
def j_cigar(self):
return ''.join(funcs.get_cigar(
self.germline[-self.post_cdr3_length:],
self.sequence[-self.post_cdr3_length:]
))