def call_debruijn_graph(self, windows, reads):
"""Helper function to call debruijn_graph module."""
windows_haplotypes = []
# Build and process de-Bruijn graph for each window.
for window in windows:
if window.end - window.start > self.config.ws_config.max_window_size:
continue
if not self.ref_reader.is_valid_interval(window):
continue
ref = self.ref_reader.bases(window)
# redacted
dbg_reads = [
read for read in reads
if ranges.ranges_overlap(window, utils.read_range(read))
]
with timer.Timer() as t:
graph = debruijn_graph.build(ref, dbg_reads,
self.config.dbg_config)
graph_building_time = t.GetDuration()
if not graph:
candidate_haplotypes = [ref]
else:
candidate_haplotypes = graph.candidate_haplotypes()
if candidate_haplotypes and candidate_haplotypes != [ref]:
candidate_haplotypes_info = realigner_pb2.CandidateHaplotypes(
span=window, haplotypes=candidate_haplotypes)
windows_haplotypes.append(candidate_haplotypes_info)
self.diagnostic_logger.log_graph_metrics(window, graph,
candidate_haplotypes,
graph_building_time)
return windows_haplotypes
def query(self, region):
"""Iterate over records overlapping a query region.
Args:
region: third_party.nucleus.protos.Range, query region.
Returns:
An iterator over third_party.nucleus.protos.Read
"""
# redacted
return (read for read in self.reads
if ranges.ranges_overlap(region, read_range(read)))
def query(self, region):
"""Iterate over records overlapping a query region.
Args:
region: learning.genomics.deepvariant.core.genomics.Range, query region.
Returns:
An iterator over learning.genomics.deepvariant.core.genomics.Read
"""
# redacted
return (read for read in self.reads
if ranges.ranges_overlap(region, read_range(read)))
def check_overlaps(chr1, start1, end1, chr2, start2, end2, expected): i1 = ranges.make_range(chr1, start1, end1) i2 = ranges.make_range(chr2, start2, end2) self.assertEquals(ranges.ranges_overlap(i1, i2), expected) self.assertEquals(ranges.ranges_overlap(i2, i1), expected)
def _fake_query(region):
return [
variant for variant in variants if ranges.ranges_overlap(
variantutils.variant_range(variant), region)
]