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Added slow5 parser #220

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wants to merge 46 commits into from
Closed

Added slow5 parser #220

wants to merge 46 commits into from

Commits on Oct 29, 2021

  1. Added slow5 parser

    Keoni Gandall committed Oct 29, 2021
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Commits on Oct 31, 2021

  1. add package docs

    Keoni Gandall committed Oct 31, 2021
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  2. Changed attributes to a map

    Keoni Gandall committed Oct 31, 2021
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  3. 100% test coverage and docs

    Keoni Gandall committed Oct 31, 2021
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  4. Added examples

    Keoni Gandall committed Oct 31, 2021
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Commits on Jun 21, 2022

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Commits on Jun 29, 2022

  1. Create tweet.yml

    TimothyStiles committed Jun 29, 2022
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  2. Update tweet.yml

    TimothyStiles committed Jun 29, 2022
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Commits on Jul 16, 2022

  1. Update tweet.yml

    TimothyStiles committed Jul 16, 2022
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Commits on Sep 6, 2022

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Commits on Sep 11, 2022

  1. Replaced the Seqhash sequencetype with Struct type argument instead o…

    …f a plain string.. (#264)
    
    * Replaced the Seqhash sequencetype with Struct type argument instead of a plain string..
    
    * Cleared the linting errors for Go > 1.16 where ioutils package has been depreciated
    
    Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
    rkrishnasanka and TimothyStiles committed Sep 11, 2022
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Commits on Sep 12, 2022

  1. fix: Use SliceStable to sort potential changes (#265)

    * fix: Use SliceStable to sort potential changes
    
    Fixes golang/go#55009
    
    Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
    Jorropo and TimothyStiles committed Sep 12, 2022
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  2. Update README.md

    TimothyStiles committed Sep 12, 2022
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  3. created config for gitpod. (#266)

    * created config for gitpod.
    
    * removed non-existent vscode extennsions.
    
    * fixed yml spacing.
    TimothyStiles committed Sep 12, 2022
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Commits on Sep 19, 2022

  1. WIP: drafted intro and io tutorials. Added templates for README and s…

    …everal other tutorials. (#267)
    
    * drafted intro and io tutorials. Added templates for README and several other tutorials.
    
    * added logic for tutorial workspace setup detection.
    
    * added todos to unwritten tutorial placeholders.
    TimothyStiles committed Sep 19, 2022
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  2. Update README.md

    TimothyStiles committed Sep 19, 2022
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  5. replacing code with gp-code (#268)

    * now using gp-code instead of code for opening tutorial windows.
    
    * added more to input output tutorial.
    TimothyStiles committed Sep 19, 2022
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Commits on Sep 20, 2022

  1. gitpod tutorial commands on startup. (#269)

    * added explicit wait for tutorial startup
    
    * added comment with issue explaining vscode -r bug.
    TimothyStiles committed Sep 20, 2022
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  2. Update .gitpod.yml

    TimothyStiles committed Sep 20, 2022
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Commits on Sep 21, 2022

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Commits on Sep 25, 2022

  1. Install Go Analysis Tools in Gitpod workspace (#270)

    * Install Go Analysis Tools
    
    Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
    lgruen and TimothyStiles committed Sep 25, 2022
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Commits on Sep 26, 2022

  1. Open tutorial README in Gitpod (#271)

    * Open tutorial README in Gitpod
    
    * Install godef
    lgruen committed Sep 26, 2022
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Commits on Sep 29, 2022

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Commits on Oct 15, 2022

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Commits on Oct 17, 2022

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  2. fixed typo.

    TimothyStiles committed Oct 17, 2022
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Commits on Oct 18, 2022

  1. fixed typo in comments.

    TimothyStiles committed Oct 18, 2022
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Commits on Nov 10, 2022

  1. Typo in tutorial (#281)

    jxilt committed Nov 10, 2022
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Commits on Nov 27, 2022

  1. Fix README installation method (#282)

    New go modules requires version.
    soypat committed Nov 27, 2022
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Commits on Nov 29, 2022

  1. Update README.md

    TimothyStiles committed Nov 29, 2022
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  2. transform: performance and test upgrades (#283)

    * added transform tests
    * added benchmarks
    * runs 8-10X faster than previous implementation
    
    
    Co-authored-by: Tim <TimothySStiles@gmail.com>
    Co-authored-by: Timothy Stiles <tim@stiles.io>
    3 people committed Nov 29, 2022
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Commits on Dec 15, 2022

  1. fasta rework (#284)

    * add more fasta.Parser API
    
    * add uniprot fasta creation
    
    * add maxLineSize argument to Parser
    
    * no EOF newline now invalidates fasta
    
    * parse now uses parseall behind the scenes.
    
    * fixed fasta.Build to output proper whitespace.
    
    * return to EOF as parse error state, fix some other stuff
    
    * fix Concurrent functions, ensure they close their readers
    
    Co-authored-by: Timothy Stiles <tim@stiles.io>
    soypat and TimothyStiles committed Dec 15, 2022
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Commits on Dec 19, 2022

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Commits on Jan 11, 2023

  1. update copyright year.

    TimothyStiles committed Jan 11, 2023
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Commits on Feb 6, 2023

  1. adding new alignment package and global alignment via Needleman-Wunsch (

    #288)
    
    * initial implementation of global alignment via NeedlemanWunsch
    
    * test coverage 100%
    
    * added wikipedia link for Needleman-Wunsch
    
    * added corner case tests at the suggestion of Daniel Liu @daniel_c0deb0t via twitter
    TimothyStiles committed Feb 6, 2023
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Commits on Feb 20, 2023

  1. Update LICENSE

    TimothyStiles committed Feb 20, 2023
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Commits on Feb 24, 2023

  1. Smith-Waterman Algorithm (#292)

    Co-authored-by: Timothy Stiles <tim@stiles.io>
    ragnorc and TimothyStiles committed Feb 24, 2023
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Commits on Feb 25, 2023

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Commits on Mar 9, 2023

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Commits on Mar 21, 2023

  1. fix comment typos (#296)

    ysung6 committed Mar 21, 2023
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Commits on Mar 23, 2023

  1. Merge branch 'main' into slow5

    Keoni Gandall committed Mar 23, 2023
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