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minor: make-pif speed up #4576

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alpapan opened this issue Sep 18, 2024 · 0 comments
Open

minor: make-pif speed up #4576

alpapan opened this issue Sep 18, 2024 · 0 comments
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@alpapan
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alpapan commented Sep 18, 2024

When using jbrowse make-pif --csi it takes a few minutes with most going into the sort|bgzip command

We could provide options to speed up

  • sort: --tmpdir the tmp directory for sort (-T) (e.g. user could provide /dev/shm)
  • sort: or a memory option --buffer-size 2G.
  • bgzip: --threads (as not all sort implementations have a parallel option)

This is for @jbrowse/cli/2.15.1 linux-x64 node-v20.16.0

@alpapan alpapan added the bug Something isn't working label Sep 18, 2024
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