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RFE: parallelized CBS (ParDNAcopy) #97

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lbeltrame opened this issue Nov 4, 2022 · 1 comment
Open

RFE: parallelized CBS (ParDNAcopy) #97

lbeltrame opened this issue Nov 4, 2022 · 1 comment

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@lbeltrame
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A possible improvement in segmentation speed would be to use ParDNAcopy to parallelize the actual CBS.

Pros:

  • Gets things done quicker (always a plus)
  • Setting a random seed (in ParDNAcopy::parSegment) allows more reproducible resutls

Cons:

  • One more dependency
  • No more updates since 2014 (it's not like DNAcopy got much love either, though)

Again, if this is deemed worthwhile I'm willing to actually implement that.

@matthdsm
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matthdsm commented Nov 4, 2022

Hi Luca,

Away on holidays atm, but we welcome each improvement you can throw at us!
I'm finishing up some other stuff over at nf-core and then I'll re-focus on wisecondorx for a while.
I've got some code improvements in the pipeline and it'd be nice to have some kind of CI here so we don't regress while adding new functionality.

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