INNER CODE UNIT · Python

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cbg-ethz/V-pipe · workflow/scripts/alignmentIntervals.py:121

            start = max(0, start - offset - 1)
            # In order to identify the region which is covered by at least
            # two windows, add to the end of the first window the
            # increment multiply by the number of windows - 2 (i.e.,
            # discarding last window). In this case assuming half-open
            # interval [start, end)
            end = min(reference_len, start_ + win_len + (num_windows - 2) * win_shift)

        return reference_name, start, end

    aux = region.split(",")
    reference_name = []
    interval = []
    for s in aux:
        ref_, start_, end_ = parse_region_aux(
            s, shorah, reference_file, win_len, win_shift
        )
        reference_name.append(ref_)

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