def intervals(self):
if self.bed_file is None:
return {}
if not self.bed_file.exists:
raise ValueError(f"can not find the bed file: {self.bed_file}")
intervals = defaultdict(list)
with open(self.bed_file) as fp:
for line in fp:
chrom, start, end, *_ = line.strip().split('\t')
intervals[chrom].append(
Interval(int(start), int(end), chrom=chrom))
return {chrom: Interval.merge(intervals[chrom]) for chrom in intervals}
def within_interval(self, segment):
if not self.intervals:
return True
if segment.reference_name not in self.intervals:
return False
current_position = Interval(
segment.reference_start or 0,
segment.reference_end
or segment.reference_start + segment.query_length,
chrom=segment.reference_name)
for interval in self.intervals[segment.reference_name]:
if interval.distance(current_position) < self.flank_size:
return True
return False
