def read_range(read):
"""Creates a Range proto from the alignment of Read.
Args:
read: nucleus.genomics.v1.Read. The read to calculate the range for.
Returns:
A nucleus.genomics.v1.Range for read.
"""
start = read.alignment.position.position
end = start + cigar.alignment_length(read.alignment.cigar)
return ranges.make_range(read.alignment.position.reference_name, start, end)
def read_range(read):
"""Creates a Range proto from the alignment of Read.
Args:
read: the read to calculate range
Returns:
A third_party.nucleus.protos.Range for read.
"""
start = read.alignment.position.position
end = start + cigar.alignment_length(read.alignment.cigar)
return ranges.make_range(read.alignment.position.reference_name, start,
end)
def test_alignment_length(self, cigar_str, expected):
cigar_units = cigar.parse_cigar_string(cigar_str)
self.assertEqual(cigar.alignment_length(cigar_units), expected)