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pangolin v2.4
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@aineniamh aineniamh released this 29 Apr 16:30
· 453 commits to master since this release
v2.4
4fc674f

Release notes

Updates to pangolearn.smk:

  • Now only map a single time producing a sam file, resulting in speed ups to pangolin
  • gofasta now muiltithreading, additional speedups

Updates to output file:

  • Output 'conflict' rather than 'probability' now, this is a measure of conflicts within the decision tree, 0 being equivalent to no conflicts, but not a confidence score.
  • Output the pango-designation version number now, which is available from pangoLEARN version 2021-04-28 onwards.

Bug fixes:

  • Noted discrepancies between minimap -a and minimap without the -a flag, leading to occasional sequences not accounted for in output csv file. This only occured when minimap2 fails to map very diverged sequences, but this is now being accounted for.
  • In --no-temp mode, minimap redirection was causing pangolin to break, now no longer re-direct this output, so appears on screen, but pipeline doesn't break.
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