Code

Covbuildmerge#89

Code

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johnlees merged 13 commits intomasterbacpop/ska.rust:masterfrom covbuildmergebacpop/ska.rust:covbuildmergeCopy head branch name to clipboardJan 27, 2025

+203-88

Commits

Commits on Jan 20, 2025

• Elided lifetimes as per clippy warnings

  jhellewell14

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  1df31e3

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• Fixed all clippy warnings in src and tests

  jhellewell14

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  1876597

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• Rewrote function any_fastq as an iterator

  jhellewell14

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  755b6ce

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• Added very explicitly written logic to choose a minimum kmer count for filtering depending on whether the user has specified their own value or if there are enough fastq files to fit the mixture model

  jhellewell14

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  41fdd25

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Commits on Jan 21, 2025

• Number of kmers can now be auto, which calculates the minimum kmers or a value passed by user

  jhellewell14

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  e2c734c

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• min kmer count now has to be >= 1 and not 5

  jhellewell14

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  3da92ff

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• Moved 64/128 represenation variable around, commented code

  jhellewell14

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  dae4945

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Commits on Jan 22, 2025

• Changed min-kmer input to an option enum that handles some parsing in cli.rs and tidied code in lib.rs by moving min-kmer logic to io_utils.rs

  jhellewell14

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  a30398d

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• Fixing clippy warnings

  jhellewell14

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  0c46767

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• Wrote a test that runs ska on the example file specifying auto for the --min-count flag

  jhellewell14

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  d0095f9

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• Added test that expects failure if you ask for a min-kmer count below 1

  jhellewell14

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  b06fdca

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Commits on Jan 27, 2025

• Made kmer_min_cutoff generic over types that implement UInt

  jhellewell14

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  d45e944

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• Moved quality definition out of if statement to reduce repeated code. Had to make quality mutable

  jhellewell14

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  394edf1

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