def clip(self, read):
""" trim a read """
first_base_pos = self.start_trim_dict.get(read.qname, 0)
last_base_pos = self.end_trim_dict.get(read.qname, -1)
# cache original details, otherwise they go to None
seq, qual, cig, end_pos = read.seq, read.qual, read.cigar, read.aend
if first_base_pos:
self.stats.start_trim(self.external_id)
read.seq = seq[first_base_pos:]
read.qual = qual[first_base_pos:]
read.cigar = cigar.trim_cigar(cig, len(read.seq), start=True)
read.pos = end_pos - cigar.ref_length(read.cigar)
assert read.aend == end_pos
# recache new stuff and recalculate last base
seq, qual, cig, end_pos = read.seq, read.qual, read.cigar, read.aend
if last_base_pos != -1:
last_base_pos = last_base_pos - first_base_pos
if last_base_pos != -1:
self.stats.end_trim(self.external_id)
read.seq = seq[:last_base_pos]
read.qual = qual[:last_base_pos]
read.cigar = cigar.trim_cigar(cig, len(read.seq))
return read
def clip(self, read):
""" clip a read to the trim locations of this amplicon """
# calculate where to clip
posns = read.positions
first_base_pos = self._find_position(self.trim_start, posns)
last_base_pos = self._find_position(self.trim_end, posns, lower=False)
# exlude primer only reads
# TODO: may be better to check the read start end for this
if not (first_base_pos or last_base_pos):
return None
# cache original details, otherwise they go to None
seq, qual, cig, end_pos = read.seq, read.qual, read.cigar, read.aend
# pileup position ignores soft clips, so remove
cig, seq, qual = cigar.remove_soft(cig, seq, qual)
if first_base_pos:
self.stats.start_trim(self.external_id)
read.seq = seq[first_base_pos:]
if qual:
read.qual = qual[first_base_pos:]
read.cigar = cigar.trim_cigar(cig, len(read.seq), start=True)
read.pos = end_pos - cigar.ref_length(read.cigar)
assert read.aend == end_pos
# recache new stuff and recalculate last base
seq, qual, cig, end_pos = read.seq, read.qual, read.cigar, read.aend
if last_base_pos is not None:
last_base_pos = last_base_pos - first_base_pos
if last_base_pos is not None:
self.stats.end_trim(self.external_id)
read.seq = seq[:last_base_pos]
if qual:
read.qual = qual[:last_base_pos]
read.cigar = cigar.trim_cigar(cig, len(read.seq))
return read