def iterator_filter_overlapping_query(psls, options):
'''remove alignments that overlap on query.
If multiple alignments overlap, the one with the highest number
of matching nucleotides is chosen.
'''
# note: only takes the full ranges, but does not check for
# individual overlap of blocks use connected components and
# hasAlignmentOverlap
ninput, noutput, ndiscarded = 0, 0, 0
last_contig = None
for block in Blat.iterator_query_overlap(
psls,
options.threshold_merge_distance):
# commented code is for base-level filtering, which is very slow
# disabled for now
# if block[0].mQueryId != last_contig:
# last_contig = block[0].mQueryId
# E.info( "processing %s" % last_contig )
l = len(block)
ninput += l
if l > 1:
ndiscarded += l
# components = Blat.getComponents( block, by_query = True )
# for component in components:
# m = [ block[x] for x in component ]
# m.sort( key = lambda x: -x.mNMatches )
# ndiscarded += len(m) - 1
# yield m[0]
# noutput += 1
else:
yield block[0]
noutput += 1
E.info("iterator_filter_overlapping_query: ninput=%i, "
"noutput=%i, ndiscarded=%i" %
(ninput, noutput, ndiscarded))
def iterator_filter_overlapping_query(psls, options):
'''remove alignments that overlap on query.
If multiple alignments overlap, the one with the highest number
of matching nucleotides is chosen.
'''
# note: only takes the full ranges, but does not check for
# individual overlap of blocks use connected components and
# hasAlignmentOverlap
ninput, noutput, ndiscarded = 0, 0, 0
last_contig = None
for block in Blat.iterator_query_overlap(psls,
options.threshold_merge_distance):
# commented code is for base-level filtering, which is very slow
# disabled for now
# if block[0].mQueryId != last_contig:
# last_contig = block[0].mQueryId
# E.info( "processing %s" % last_contig )
l = len(block)
ninput += l
if l > 1:
ndiscarded += l
# components = Blat.getComponents( block, by_query = True )
# for component in components:
# m = [ block[x] for x in component ]
# m.sort( key = lambda x: -x.mNMatches )
# ndiscarded += len(m) - 1
# yield m[0]
# noutput += 1
else:
yield block[0]
noutput += 1
E.info("iterator_filter_overlapping_query: ninput=%i, "
"noutput=%i, ndiscarded=%i" % (ninput, noutput, ndiscarded))
