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Ambiguous base filter #39

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esteinig opened this issue Jul 14, 2023 · 2 comments
Open
4 tasks

Ambiguous base filter #39

esteinig opened this issue Jul 14, 2023 · 2 comments
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@esteinig
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enhancement New feature or request next release

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@esteinig
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Requested by @mbhall88

  • Remove reads with > x % ambiguous bases
  • Command line option for filter and allowed bases
  • Speed optimisation [will have to have a look]
  • Tests
@esteinig esteinig added the enhancement New feature or request label Jul 14, 2023
@esteinig esteinig self-assigned this Jul 14, 2023
@mbhall88
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mbhall88 commented Aug 2, 2023

In the meantime, Wei Shen is awesome and there is (of course) a way to do this with seqkit shenwei356/seqkit#403

@esteinig
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esteinig commented Aug 5, 2023 •
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Love Wei Shen's work - and of course it was available ^^ I'll flag this for the next version.

There should be a fast way of doing this using the &[u8] sequence from a needletail record.

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