def parse(bamfile, minqual):
bamhandle = AlignmentFile(bamfile, 'rb')
positions = Positions()
for read in bamhandle:
if isclip(read) is False or read.mapping_quality < minqual:
continue
clip = ClipRead(read)
pos = positions.getposition(bamhandle.get_reference_name(read.reference_id), \
clip.getclippos())
pos.addclipread(clip)
bamhandle.close()
return positions
if min_idy > 0.:
assert r.has_tag('NM')
if r.has_tag('NM'):
#idy=identity(r.reference_length, r.get_tag('NM'))
idy = identity(r.reference_length + insertion_cnt(r.cigartuples),
r.get_tag('NM'))
#idy=identity(r.query_alignment_length, r.get_tag('NM'))
else:
idy = 1.
if idy < min_idy:
continue
if args.targets:
if alignment.get_reference_name(r.reference_id) not in targets:
continue
init_length = r.infer_read_length()
if not check_query_cov(r, init_length, alignment.lengths[r.reference_id]):
continue
if r.is_reverse:
clipped_suffix, _ = hard_clipped(r.cigartuples)
query_alignment_start = init_length - r.query_alignment_end - clipped_suffix
query_alignment_end = init_length - r.query_alignment_start - clipped_suffix
reference_start_str = "(%d" % r.reference_end
reference_end_str = "%d]" % r.reference_start
else:
clipped_prefix, _ = hard_clipped(r.cigartuples)
query_alignment_start = r.query_alignment_start + clipped_prefix
