def call_aligner(self, assembled_region):
"""Helper function to call aligner module."""
if not assembled_region.reads:
return []
contig = assembled_region.region.reference_name
ref_start = max(
0,
min(assembled_region.read_span.start, assembled_region.region.start) -
_REF_ALIGN_MARGIN)
ref_end = min(
self.ref_reader.contig(contig).n_bases,
max(assembled_region.read_span.end, assembled_region.region.end) +
_REF_ALIGN_MARGIN)
ref_prefix = self.ref_reader.query(
ranges.make_range(contig, ref_start, assembled_region.region.start))
ref = self.ref_reader.query(assembled_region.region)
# If we can't create the ref suffix then return the original alignments.
if ref_end <= assembled_region.region.end:
return assembled_region.reads
else:
ref_suffix = self.ref_reader.query(
ranges.make_range(contig, assembled_region.region.end, ref_end))
ref_region = ranges.make_range(contig, ref_start, ref_end)
ref_seq = ref_prefix + ref + ref_suffix
reads_aligner = aligner.Aligner(self.config.aln_config, ref_region, ref_seq)
return reads_aligner.align_reads([
ref_prefix + target + ref_suffix
for target in assembled_region.haplotypes
], assembled_region.reads)
def make_test_aligner(self, ref_seq=None, region=None):
config = realigner_pb2.RealignerOptions.AlignerOptions(match=1,
mismatch=1,
gap_open=2,
gap_extend=1,
k=3,
error_rate=.02)
ref_seq = ref_seq or 'AAAAAAA'
region = region or ranges.make_range('ref', 10, 10 + len(ref_seq))
return aligner.Aligner(config, region, ref_seq)
