def check_overlaps(chr1, start1, end1, chr2, start2, end2, expected):
nbp = end1 - start1
read = test_utils.make_read(
'A' * nbp, chrom=chr1, start=start1, cigar='{}M'.format(nbp))
region = ranges.make_range(chr2, start2, end2)
self.assertEqual(utils.read_overlaps_region(read, region), expected)
# This check ensures we get the same result calling ranges.ranges_overlap.
self.assertEqual(
ranges.ranges_overlap(region, utils.read_range(read)), expected)
def query(self, region):
"""Returns an iterator for going through the reads in the region.
Args:
region: nucleus.genomics.v1.Range. The query region.
Returns:
An iterator over nucleus.genomics.v1.Read protos.
"""
# TODO(b/37353140): Add a faster query version for sorted reads.
return (read for read in self.reads
if ranges.ranges_overlap(region, utils.read_range(read)))
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: nucleus.genomics.v1.Range, the query region.
Returns:
An iterator over nucleus.genomics.v1.Read's.
"""
# TODO(b/37353140): Add a faster query version for sorted reads.
return (read for read in self.reads
if ranges.ranges_overlap(region, utils.read_range(read)))
def variants_overlap(variant1, variant2):
"""Returns True if the range of variant1 and variant2 overlap.
This is equivalent to:
ranges_overlap(variant_range(variant1), variant_range(variant2))
Args:
variant1: nucleus.genomics.v1.Variant we want to compare for overlap.
variant2: nucleus.genomics.v1.Variant we want to compare for overlap.
Returns:
True if the variants overlap, False otherwise.
"""
return ranges.ranges_overlap(variant_range(variant1), variant_range(variant2))
def query(self, region):
return iter(variant for variant in self.variants
if ranges.ranges_overlap(
variant_utils.variant_range(variant), region))
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.assertEqual(ranges.ranges_overlap(i1, i2), expected)
self.assertEqual(ranges.ranges_overlap(i2, i1), expected)
