def make_range(chrom, start, end):
"""Returns a nucleus.genomics.v1.Range.
Args:
chrom: str. The chromosome name.
start: int. The start position (0-based, inclusive) of this range.
end: int. The end position (0-based, exclusive) of this range.
Returns:
A nucleus.genomics.v1.Range.
"""
return range_pb2.Range(reference_name=chrom, start=start, end=end)
def make_range(chrom, start, end):
"""Creates a genomics.Range object chr:start-end.
Args:
chrom: The chromosome name as a string.
start: The start position (0-based, inclusive, integer) of this range.
end: The end position (0-based, exclusive, integer) of this range.
Returns:
A third_party.nucleus.protos.Range.
"""
return range_pb2.Range(reference_name=chrom, start=start, end=end)
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.
"""
range_pb = range_pb2.Range()
utils_cpp.read_range(read, range_pb)
return range_pb
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 range_pb2.Range(
reference_name=read.alignment.position.reference_name,
start=start,
end=end)
def read_range(read, use_cached_read_end=True):
"""Creates a Range proto from the alignment of Read.
Args:
read: nucleus.genomics.v1.Read. The read to calculate the range for.
use_cached_read_end: If True, use the `cached_end` stored in Read instead of
recalculating.
Returns:
A nucleus.genomics.v1.Range for read.
"""
range_pb = range_pb2.Range()
utils_cpp.read_range(read,
range_pb,
use_cached_read_end=use_cached_read_end)
return range_pb