Source code for iranges.interval

from typing import List, Optional, Tuple, Union

import numpy as np

__author__ = "jkanche"
__copyright__ = "jkanche"
__license__ = "MIT"




def create_np_interval_vector(
    intervals: "IRanges",
    with_reverse_map: bool = False,
    force_size: Optional[int] = None,
    dont_sum: bool = False,
    value: Union[int, float] = 1,
) -> Tuple[np.ndarray, Optional[List]]:
    """Represent intervals and calculate coverage.

    Args:
        intervals:
            Input intervals.

        with_reverse_map:
            Return map of indices? Defaults to False.

        force_size:
            Force size of the array.

        dont_sum:
            Do not sum. Defaults to False.

        value:
            Default value to increment. Defaults to 1.

    Returns:
        A numpy array representing
        coverage from the intervals and optionally the index map.
    """
    if len(intervals) == 0:
        return np.zeros(0), None

    max_end = force_size
    if max_end is None:
        max_end = intervals.get_end().max()
    else:
        max_end += 1

    _type = np.int32
    if isinstance(value, float):
        _type = np.float32

    cov = np.zeros(max_end, dtype=_type)

    revmap = None
    if with_reverse_map:
        revmap = [[] for _ in range(max_end)]

    counter = 0
    for name, row in intervals:
        _start = row.start[0]
        _end = row.end[0]

        if dont_sum:
            cov[_start:_end] = value
        else:
            cov[_start:_end] += value

        if with_reverse_map:
            _ = [
                revmap[x].append(name if name is not None else counter + 1)
                for x in range(_start, _end)
            ]

        counter += 1
    return cov[1:], revmap





def calc_gap_and_overlap(
    first: Tuple[int, int], second: Tuple[int, int]
) -> Tuple[Optional[int], Optional[int]]:
    """Calculate gap and/or overlap between two intervals.

    Args:
        first:
            Interval containing start and end positions.
            `end` is non-inclusive.

        second:
            Interval containing start and end positions.
            `end` is non-inclusive.
    """
    if min(first[1], second[1]) > max(first[0], second[0]):
        _overlap = min(first[1], second[1]) - max(first[0], second[0])
        return (None, _overlap)

    _gap = None
    if second[0] >= first[1]:
        _gap = second[0] - first[1]
    elif first[0] >= second[1]:
        _gap = first[0] - second[1]

    return (_gap, None)