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[EXP] add sourmash distance estimation #1788

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Closed

[EXP] add sourmash distance estimation #1788

wants to merge 46 commits into from

Commits on Jan 13, 2022

  1. init dist utils

    @bluegenes
    bluegenes committed Jan 13, 2022
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  2. add confidence tests

    @bluegenes
    bluegenes committed Jan 13, 2022
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  3. optionally return sim/ident instead

    @bluegenes
    bluegenes committed Jan 13, 2022
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  4. add ani estimation to signature

    @bluegenes
    bluegenes committed Jan 13, 2022
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  5. return confidence interval in addition to point estimate

    @bluegenes
    bluegenes committed Jan 13, 2022
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Commits on Jan 14, 2022

  1. return ANI from compare

    @bluegenes
    bluegenes committed Jan 14, 2022
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  2. add containment ANI tests to test_compare

    @bluegenes
    bluegenes committed Jan 14, 2022
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  3. init compare ANI tests

    @bluegenes
    bluegenes committed Jan 14, 2022
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  4. add option

    @bluegenes
    bluegenes committed Jan 14, 2022
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  5. ani in prefetch and gather

    @bluegenes
    bluegenes committed Jan 14, 2022
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  6. test ani from precalculated score

    @bluegenes
    bluegenes committed Jan 14, 2022
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  7. return_ANI --> return_ani 

    Co-authored-by: C. Titus Brown <titus@idyll.org>
    @bluegenes @ctb
    bluegenes and ctb committed Jan 14, 2022
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  8. remaining return_ANI changes

    @bluegenes
    bluegenes committed Jan 14, 2022
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  9. cleanup unused fn

    @bluegenes
    bluegenes committed Jan 14, 2022
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  10. spacing

    @bluegenes
    bluegenes committed Jan 14, 2022
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Commits on Jan 17, 2022

  1. fix mc kmers

    @bluegenes
    bluegenes committed Jan 17, 2022
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  2. add corresponding mh methods

    @bluegenes
    bluegenes committed Jan 17, 2022
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  3. merge in latest

    @bluegenes
    bluegenes committed Jan 17, 2022
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  4. round kmers for jaccard

    @bluegenes
    bluegenes committed Jan 17, 2022
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Commits on Jan 18, 2022

  1. allow confidence tuning

    @bluegenes
    bluegenes committed Jan 18, 2022
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Commits on Jan 19, 2022

  1. enable bp --> ANI

    @bluegenes
    bluegenes committed Jan 19, 2022
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  2. fix c to dist in search

    @bluegenes
    bluegenes committed Jan 19, 2022
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  3. optionally estimate query ani while summarizing gather results

    @bluegenes
    bluegenes committed Jan 19, 2022
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  4. addl cols in gatherresult

    @bluegenes
    bluegenes committed Jan 19, 2022
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Commits on Jan 20, 2022

  1. addl prefetch cols; test ani in summarize_gather_at

    @bluegenes
    bluegenes committed Jan 20, 2022
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  2. add tests for ani_threshold

    @bluegenes
    bluegenes committed Jan 20, 2022
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  3. fix typo

    @bluegenes
    bluegenes committed Jan 20, 2022
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  4. addl tests

    @bluegenes
    bluegenes committed Jan 20, 2022
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  5. report CI in prefetch, gather bc I wants them for testing

    @bluegenes
    bluegenes committed Jan 20, 2022
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Commits on Jan 25, 2022

  1. estimate ANI during search

    @bluegenes
    bluegenes committed Jan 25, 2022
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Commits on Jan 26, 2022

  1. search_scaled

    @bluegenes
    bluegenes committed Jan 26, 2022
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  2. wade into downsampling

    @bluegenes
    bluegenes committed Jan 26, 2022
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  3. dist comment

    @bluegenes
    bluegenes committed Jan 26, 2022
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Commits on Feb 2, 2022

  1. handle downsampling in minhash, signature ANI fns

    @bluegenes
    bluegenes committed Feb 2, 2022
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  2. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Feb 2, 2022
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Commits on Feb 8, 2022

  1. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Feb 8, 2022
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Commits on Feb 9, 2022

  1. whoops, fix rogue test

    @bluegenes
    bluegenes committed Feb 9, 2022
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  2. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Feb 9, 2022
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Commits on Mar 8, 2022

  1. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Mar 8, 2022
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Commits on Mar 12, 2022

  1. Add dist est (#1860) 

    * enabled running main

* added point estimate and error bound

* added docstring

* added usage code

* added nothing_common code, usage, docstrings, tested
    @mahmudhera
    mahmudhera committed Mar 12, 2022
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  2. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Mar 12, 2022
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  3. enable just point estimate for distance_to_identity

    @bluegenes
    bluegenes committed Mar 12, 2022
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Commits on Mar 13, 2022

  1. save in progress changes

    @bluegenes
    bluegenes committed Mar 13, 2022
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Commits on Apr 1, 2022

  1. upd

    @bluegenes
    bluegenes committed Apr 1, 2022
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Commits on Apr 2, 2022

  1. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Apr 2, 2022
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Commits on Apr 15, 2022

  1. Merge branch 'latest' into add-dist-est

    @bluegenes
    bluegenes committed Apr 15, 2022
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