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count_overlaps documentation says it supports nb_cpu but it is not implemented #363

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leetaiyi opened this issue Nov 1, 2023 · 1 comment

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@leetaiyi
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leetaiyi commented Nov 1, 2023

pyranges_main.py, line 1294

def count_overlaps(
     self,
     other,
     strandedness=None,
     keep_nonoverlapping=True,
     overlap_col="NumberOverlaps",
 ):
     """Count number of overlaps per interval.

     Count how many intervals in self overlap with those in other.

     Parameters
     ----------
     strandedness : {"same", "opposite", None, False}, default None, i.e. auto

         Whether to perform the operation on the same, opposite or no strand. Use False to
         ignore the strand. None means use "same" if both PyRanges are stranded, otherwise
         ignore.

     keep_nonoverlapping : bool, default True

         Keep intervals without overlaps.

     overlap_col : str, default "NumberOverlaps"

         Name of column with overlap counts.

     nb_cpu : int, default 1

         How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple.
         Will only lead to speedups on large datasets.
@leetaiyi leetaiyi changed the title count_overlaps documentation says it supports nb_cores but it is not implemented count_overlaps documentation says it supports nb_cpu but it is not implemented Nov 1, 2023
@endrebak
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endrebak commented Nov 3, 2023

nb_cpu is going to be removed. There really is no speedup from it now that all the functions are super-fast

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