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Seeding and chaining optimizations#400

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hmusta merged 45 commits intomasterfrom
hm/chain_optim
Sep 12, 2022
Merged

Seeding and chaining optimizations#400
hmusta merged 45 commits intomasterfrom
hm/chain_optim

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@hmusta hmusta commented Apr 13, 2022

  • Filter out low complexity seeds using sdust
  • Optimize chainer: reduce memory overhead
  • AVX2 instructions in chainer
  • Simplify labeled seeding
  • Unit tests

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Could you also write in docs some guidelines for the choice of parameters?

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hmusta commented Jun 17, 2022

I set up the unit tests for chaining, now I just need to add a few more to test corner cases.

@hmusta hmusta requested a review from karasikov June 17, 2022 16:14
hmusta and others added 3 commits July 12, 2022 11:42
Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>
@hmusta hmusta requested a review from karasikov July 13, 2022 12:16
hmusta and others added 5 commits September 12, 2022 01:29
Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>
Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>
Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>
* Added unit tests for RowDiff
@hmusta hmusta merged commit bcd4adc into master Sep 12, 2022
@hmusta hmusta deleted the hm/chain_optim branch September 12, 2022 10:20
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2 participants