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[MRG] add lca DBs as inputs to 'sourmash search' and 'gather' #533

Merged
merged 21 commits into from
Dec 19, 2018
Merged

[MRG] add lca DBs as inputs to 'sourmash search' and 'gather' #533

merged 21 commits into from
Dec 19, 2018

Commits on Aug 18, 2018

  1. add lca DBs to 'sourmash search' and 'gather'

    @ctb
    ctb committed Aug 18, 2018
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  2. extract signatures once, at the cost of more memory

    @ctb
    ctb committed Aug 18, 2018
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Commits on Oct 15, 2018

  1. Merge branch 'master' into add/search_gather_lca_db

    @luizirber
    luizirber authored Oct 15, 2018
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Commits on Dec 12, 2018

  1. [WIP] Refactor LCA database to contain all the information. (#537) 

    * a trial refactoring of the lca db

* save and load seem to basically work

* got search & gather on LCA working in new framework

* allow key error

* keep identities with no lineage assigment

* add multigather

* Hyperlink DOIs to preferred resolver (#562)

* fix divide by zero issue in MinHash.contained_by (#572)

* fix divide by zero issue in contained_by

* remove unused lineages and identifiers

* update report output

* majority of lca tests passing now!

* fix gather?

* ...all tests pass?
    @ctb
    ctb authored Dec 12, 2018
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  2. Merge branch 'master' of github.com:dib-lab/sourmash into add/search_… 

    …gather_lca_db
    @ctb
    ctb committed Dec 12, 2018
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  3. flag older LCA DBs

    @ctb
    ctb committed Dec 12, 2018
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  4. some cleanup

    @ctb
    ctb committed Dec 12, 2018
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Commits on Dec 13, 2018

  1. restore py27 compat

    @ctb
    ctb committed Dec 13, 2018
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  2. minor cleanup and commenting

    @ctb
    ctb committed Dec 13, 2018
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  3. add test for old-format LCA DB

    @ctb
    ctb committed Dec 13, 2018
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  4. bump lca_db version to 2

    @ctb
    ctb committed Dec 13, 2018
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  5. fix situation where json provides a list rather than a dictionary

    @ctb
    ctb committed Dec 13, 2018
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Commits on Dec 14, 2018

  1. add test coverage

    @ctb
    ctb committed Dec 14, 2018
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Commits on Dec 15, 2018

  1. provide some more pythonic & succinct test code; add some more lca tests

    @ctb
    ctb committed Dec 15, 2018
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  2. Merge branch 'master' of github.com:dib-lab/sourmash into add/search_… 

    …gather_lca_db
    @ctb
    ctb committed Dec 15, 2018
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  3. some tests of sourmash search and gather on LCA dbs

    @ctb
    ctb committed Dec 15, 2018
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  4. produce a useful error message for -traverse-directory with no --forc… 

    …e on lca index
    @ctb
    ctb committed Dec 15, 2018
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  5. fix py27

    @ctb
    ctb committed Dec 15, 2018
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Commits on Dec 17, 2018

  1. add a notify at beginning of load SBTs

    @ctb
    ctb committed Dec 17, 2018
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  2. use a faster method for checking for empty minhashes

    @ctb
    ctb committed Dec 17, 2018
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Commits on Dec 18, 2018

  1. update links to latest databases

    @ctb
    ctb committed Dec 18, 2018
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