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Properly handling Ns in make_prg #60

Merged
merged 6 commits into from
Jul 17, 2023
Merged

Properly handling Ns in make_prg #60

merged 6 commits into from
Jul 17, 2023

Commits on Jul 11, 2023

  1. Instead of ignoring Ns in the MSA, we now replace N with the consensus 

    of each column. If the whole column is N and/or gaps, we replace it by a random base, with the seed initialised with the alignment sequences, i.e. this replacement is reproducible if the same alignment is given.
    @leoisl
    leoisl committed Jul 11, 2023
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  2. Adding Amira test cases

    @leoisl
    leoisl committed Jul 11, 2023
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  3. just precommit

    @leoisl
    leoisl committed Jul 11, 2023
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  4. Adding another test to get_majority_consensus_from_MSA()

    @leoisl
    leoisl committed Jul 11, 2023
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Commits on Jul 13, 2023

  1. Randomly select highest-count bases, do not require upper-cased MSA and 

    refactoring
    @leoisl
    leoisl committed Jul 13, 2023
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  2. linting

    @leoisl
    leoisl committed Jul 13, 2023
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