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[MRG] Divide non-DNA MinHash ksize by 3 for external consumption. #1277

Merged
merged 41 commits into from
Jan 19, 2021
Merged

[MRG] Divide non-DNA MinHash ksize by 3 for external consumption. #1277

merged 41 commits into from
Jan 19, 2021

Commits on Jun 5, 2020

  1. start adding moltype into LCA DB construction

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    ctb committed Jun 5, 2020
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Commits on Jun 6, 2020

  1. save/load moltype in LCA database JSON

    @ctb
    ctb committed Jun 6, 2020
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  2. support all the moltypes

    @ctb
    ctb committed Jun 6, 2020
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  3. fix test <shakes head>

    @ctb
    ctb committed Jun 6, 2020
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  4. cleaned up reporting; fixed used-lineage tracking logic

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    ctb committed Jun 6, 2020
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  5. test output ksize/scaled/moltype

    @ctb
    ctb committed Jun 6, 2020
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  6. rename bug 781 sig filename

    @ctb
    ctb committed Jun 6, 2020
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  7. fix sourmash sig describe moltype output

    @ctb
    ctb committed Jun 6, 2020
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  8. remove unnecessary tempdir use

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    ctb committed Jun 6, 2020
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  9. LCA_Database.insert now returns number of hashes inserted

    @ctb
    ctb committed Jun 6, 2020
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  10. test lca database creation, search, etc. for protein, hp, dayhoff

    @ctb
    ctb committed Jun 6, 2020
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  11. command line tests for lca indexing with protein, hp, dayhoff

    @ctb
    ctb committed Jun 6, 2020
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  12. bump LCA database version number

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  13. test command line search and gather of prot/hp/dayhoff LCA databases

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  14. remove requirement for --no-dna lca index

    @ctb
    ctb committed Jun 6, 2020
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  15. refactor calculate_moltype and test

    @ctb
    ctb committed Jun 6, 2020
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  16. add sbt search/index tests for protein/hp/dayhoff

    @ctb
    ctb committed Jun 6, 2020
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  17. add full tests for sig describe on hp, dayhoff, and protein

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    ctb committed Jun 6, 2020
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  18. test behavior of lca_db.insert better

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  19. resolved comment (I did a bad copy paste)

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Commits on Jun 9, 2020

  1. protein ksizes must be divisible by 3

    @bluegenes
    bluegenes committed Jun 9, 2020
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Commits on Jun 14, 2020

  1. Merge branch 'master' into div-3

    @ctb
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Commits on Jun 15, 2020

  1. change test to assert failure with bad ksize

    @bluegenes
    bluegenes committed Jun 15, 2020
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  2. use status instead of presence of file 

    Co-authored-by: C. Titus Brown <[email protected]>
    @bluegenes @ctb
    bluegenes and ctb authored Jun 15, 2020
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Commits on Jan 16, 2021

  1. adjust output message minorly

    @ctb
    ctb committed Jan 16, 2021
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  2. divide ksize by 3 in python API

    @ctb
    ctb committed Jan 16, 2021
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  3. more better comments

    @ctb
    ctb committed Jan 16, 2021
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  4. fix 'sig' CLI tests for protein ksize

    @ctb
    ctb committed Jan 16, 2021
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  5. remove test with invalid signature file

    @ctb
    ctb committed Jan 16, 2021
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  6. fix prot ksize

    @ctb
    ctb committed Jan 16, 2021
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  7. fix Python check on k-mer size being added for protein

    @ctb
    ctb committed Jan 16, 2021
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  8. fixed protein ksize

    @ctb
    ctb committed Jan 16, 2021
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  9. fixed test to trigger correct error after prot ksize change

    @ctb
    ctb committed Jan 16, 2021
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  10. fix prot ksize

    @ctb
    ctb committed Jan 16, 2021
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  11. fix sourmash sketch tests for new ksize

    @ctb
    ctb committed Jan 16, 2021
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  12. fix prot ksize

    @ctb
    ctb committed Jan 16, 2021
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  13. Merge remote-tracking branch 'origin/div-3' into change_protein_kmer

    @ctb
    ctb committed Jan 16, 2021
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  14. make MinHash constructor obey new ksize rules

    @ctb
    ctb committed Jan 16, 2021
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  15. fix test_sbt for new prot ksize

    @ctb
    ctb committed Jan 16, 2021
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  16. Merge branch 'latest' of github.com:dib-lab/sourmash into change_prot… 

    …ein_kmer
    @ctb
    ctb committed Jan 16, 2021
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Commits on Jan 19, 2021

  1. add deprecation warnings

    @ctb
    ctb committed Jan 19, 2021
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