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[MRG] add an lca gather signature decomposition approach #390

Merged
merged 45 commits into from
Feb 23, 2018
Merged

[MRG] add an lca gather signature decomposition approach #390

merged 45 commits into from
Feb 23, 2018

Commits on Oct 31, 2017

  1. Bump version and add note pointing to stable docs

    @luizirber
    luizirber committed Oct 31, 2017
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Commits on Feb 3, 2018

  1. add an initial lca gather greedy search implementation

    @ctb
    ctb committed Feb 3, 2018
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Commits on Feb 4, 2018

  1. added gather file :)

    @ctb
    ctb committed Feb 4, 2018
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  2. cleanup, refactor

    @ctb
    ctb committed Feb 4, 2018
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  3. add some tests

    @ctb
    ctb committed Feb 4, 2018
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  4. fix output; add short TODO list

    @ctb
    ctb committed Feb 4, 2018
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  5. add output options

    @ctb
    ctb committed Feb 4, 2018
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Commits on Feb 6, 2018

  1. Merge branch 'master' of github.com:dib-lab/sourmash into add/lca_gather

    @ctb
    ctb committed Feb 6, 2018
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Commits on Feb 7, 2018

  1. don't collapse lineages

    @ctb
    ctb committed Feb 7, 2018
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  2. reworked code a bit, still not working

    @ctb
    ctb committed Feb 7, 2018
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  3. Merge branch 'master' of github.com:dib-lab/sourmash into add/lca_gather

    @ctb
    ctb committed Feb 7, 2018
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Commits on Feb 11, 2018

  1. add some docs on search, gather, and lca

    @ctb
    ctb committed Feb 11, 2018
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Commits on Feb 12, 2018

  1. updated some text

    @ctb
    ctb committed Feb 12, 2018
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  2. Fix formatting error

    @luizirber
    luizirber committed Feb 12, 2018
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Commits on Feb 13, 2018

  1. Merge branch 'master' of github.com:dib-lab/sourmash into add/lca_gather

    @ctb
    ctb committed Feb 13, 2018
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Commits on Feb 18, 2018

  1. pointed at search.format_bp

    @ctb
    ctb committed Feb 18, 2018
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  2. add check for sourmash gather fix

    @ctb
    ctb committed Feb 18, 2018
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  3. fix argparse reporting

    @ctb
    ctb committed Feb 18, 2018
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  4. Merge branch 'add/lca_gather' into add/lca_gather_2

    @ctb
    ctb committed Feb 18, 2018
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  5. added strain output; added saving of signatures_to_name

    @ctb
    ctb committed Feb 18, 2018
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  6. update tests for strain addition

    @ctb
    ctb committed Feb 18, 2018
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  7. fix genus display if _ is present

    @ctb
    ctb committed Feb 18, 2018
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  8. fix very challenging error to find :)

    @ctb
    ctb committed Feb 18, 2018
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  9. added name to lca gather output

    @ctb
    ctb committed Feb 18, 2018
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  10. output equivalent matches

    @ctb
    ctb committed Feb 18, 2018
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  11. add test for equivalent results display and csv output

    @ctb
    ctb committed Feb 18, 2018
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  12. make unassigned slightly nicer

    @ctb
    ctb committed Feb 18, 2018
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  13. update sourmash lca output

    @ctb
    ctb committed Feb 18, 2018
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  14. update sourmash lca output

    @ctb
    ctb committed Feb 18, 2018
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  15. upgrade the documentation a bunch

    @ctb
    ctb committed Feb 18, 2018
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  16. Merge branch 'docs/improvements' of github.com:dib-lab/sourmash into … 

    …doc/classify
    @ctb
    ctb committed Feb 18, 2018
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  17. cleanup foo

    @ctb
    ctb committed Feb 18, 2018
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  18. address @taylorreiter comments

    @ctb
    ctb committed Feb 18, 2018
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  19. link to LCA databases

    @ctb
    ctb committed Feb 18, 2018
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  20. provide construction details

    @ctb
    ctb committed Feb 18, 2018
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  21. Merge branch 'doc/classify' into add/lca_gather

    @ctb
    ctb committed Feb 18, 2018
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  22. Merge branch 'master' into add/lca_gather

    @ctb
    ctb committed Feb 18, 2018
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  23. fix reST in updated docs

    @ctb
    ctb committed Feb 18, 2018
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  24. Merge branch 'master' into add/lca_gather

    @ctb
    ctb committed Feb 18, 2018
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  25. Merge branch 'master' of github.com:dib-lab/sourmash into add/lca_gather

    @ctb
    ctb committed Feb 18, 2018
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  26. Merge branch 'add/lca_gather' of github.com:dib-lab/sourmash into add… 

    …/lca_gather
    @ctb
    ctb committed Feb 18, 2018
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Commits on Feb 19, 2018

  1. fix typo

    @ctb
    ctb committed Feb 19, 2018
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  2. catch parse error -> question if it's a valid LCA DB

    @ctb
    ctb committed Feb 19, 2018
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Commits on Feb 23, 2018

  1. Merge branch 'master' of github.com:dib-lab/sourmash into add/lca_gather

    @ctb
    ctb committed Feb 23, 2018
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  2. add in consistent display by name of match for both sourmash gather a… 

    …nd lca gatherc
    @ctb
    ctb committed Feb 23, 2018
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