def map_all_to_refs(self, min_band_score, **aligner_kw):
# FIXME it would be nice to only calculate bands for read v. ref not
# all pairwise of reads too
assert self.bands_indexed, 'Bands must be indexed first'
self.log('Mapping all reads against reference sequences')
reads, refs = self.load_reads(), self.load_refs()
indic = ProgressIndicator(num_total=len(reads))
indic.start()
for read in reads:
indic.progress()
rec, target_rec, aln = read.map(refs,
min_band_score=min_band_score,
**aligner_kw)
if rec is not None:
yield rec, target_rec, aln
indic.finish()
def map_all_to_all(self, min_band_score, **aligner_kw):
assert self.bands_indexed, 'Bands must be indexed first'
self.log('Mapping all reads against each other')
reads = self.load_reads() # NOTE comes in sorted order of id
indic = ProgressIndicator(num_total=len(reads))
indic.start()
for read in reads:
indic.progress()
# NOTE only compare to reads after us
others = (r.record for r in reads if r.record.id > read.record.id)
for other in others:
rec, target_rec, aln = read.map(other,
min_band_score=min_band_score,
**aligner_kw)
if rec is None:
continue
yield rec, target_rec, aln
indic.finish()