Skip to content

Workaround for overflow error mentioned in issue #20 - #23

Open
leetaiyi wants to merge 4 commits into
mortazavilab:masterfrom
leetaiyi:master
Open

Workaround for overflow error mentioned in issue #20#23
leetaiyi wants to merge 4 commits into
mortazavilab:masterfrom
leetaiyi:master

Conversation

@leetaiyi

@leetaiyi leetaiyi commented Nov 8, 2023

Copy link
Copy Markdown

If detected that the product of the sizes of df and gr_bam are over 2^31, will subset them both to avoid the overflow error. Will cause in a few lost edgecases near where the divisions are though. Now works on the cases where it failed due to this error.

Added a workaround for large intersections of df and gr_bam by splitting both into subsets based on how many more factors of 2 the product of the subset of (chr,strand) was over 2^31. Will be missing a few cases in the splits but is a reasonable workaround for now.

Included a hardcoding for nb_cpus=8
Added missing numpy import
Because Pyranges documented it was available but never implemented it >:(
Cleaned the `n$m` format to just output `n`. This is a very space-inefficient workaround, but do not know the pyranges class well enough to find a better way.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant