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io->bio #339

Closed
wants to merge 67 commits into from
Closed

io->bio #339

wants to merge 67 commits into from

Commits on Aug 24, 2023

  1. Moved io to bio

    Keoni Gandall committed Aug 24, 2023
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  2. fixed io imports

    Keoni Gandall committed Aug 24, 2023
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Commits on Aug 31, 2023

  1. Add more generic definitions to bio

    Keoni Gandall committed Aug 31, 2023
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Commits on Sep 1, 2023

  1. Update bio/fastq/fastq.go 

    Co-authored-by: Willow Carretero Chavez <[email protected]>
    @carreter
    Koeng101 and carreter committed Sep 1, 2023
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  2. update fasta

    Keoni Gandall committed Sep 1, 2023
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  3. Merge branch 'ioToBio' of github.com:TimothyStiles/poly into ioToBio

    Keoni Gandall committed Sep 1, 2023
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  4. add fasta updates and parser

    Keoni Gandall committed Sep 1, 2023
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Commits on Sep 2, 2023

  1. made readability improvements

    Keoni Gandall committed Sep 2, 2023
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  2. changed ParseWithHeader

    Keoni Gandall committed Sep 2, 2023
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  3. removed int64 in reads

    Keoni Gandall committed Sep 2, 2023
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  4. add more example tests

    Keoni Gandall committed Sep 2, 2023
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  5. gotta update this for this tests!

    Keoni Gandall committed Sep 2, 2023
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Commits on Sep 5, 2023

  1. integrate slow5

    Keoni Gandall committed Sep 5, 2023
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  2. have examples covering most of changes

    Keoni Gandall committed Sep 5, 2023
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  3. removed interfaces

    Keoni Gandall committed Sep 5, 2023
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Commits on Sep 7, 2023

  1. updated with NewXXXParser

    Keoni Gandall committed Sep 7, 2023
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  2. added 3 parsers

    Keoni Gandall committed Sep 7, 2023
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  3. added pileup

    Keoni Gandall committed Sep 7, 2023
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Commits on Sep 9, 2023

  1. add concurrent functions plus better documentation

    Keoni Gandall committed Sep 9, 2023
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Commits on Sep 11, 2023

  1. moved svb to ioToBio

    Keoni Gandall committed Sep 11, 2023
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  2. Improve tests

    Keoni Gandall committed Sep 11, 2023
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  3. make better docs for header

    Keoni Gandall committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. Update bio/fasta/fasta_test.go 

    Co-authored-by: Willow Carretero Chavez <[email protected]>
    @carreter
    Koeng101 and carreter committed Sep 12, 2023
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  2. changed name of LowLevelParser to parserInterface

    Keoni Gandall committed Sep 12, 2023
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  3. Merge branch 'main' into ioToBio

    Keoni Gandall committed Sep 12, 2023
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  4. zw -> zipWriter

    Keoni Gandall committed Sep 12, 2023
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  5. remove a identifier from pileup

    Keoni Gandall committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. genbank parser now compatible

    Keoni Gandall committed Sep 13, 2023
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  2. writeTo interface now fulfilled

    Keoni Gandall committed Sep 13, 2023
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  3. make linter happy :)

    Keoni Gandall committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. convert all types to io.WriterTo

    Keoni Gandall committed Sep 14, 2023
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  2. fixed linter issues

    Keoni Gandall committed Sep 14, 2023
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  3. handle EOF better

    Keoni Gandall committed Sep 14, 2023
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  4. fixed tutorial

    Keoni Gandall committed Sep 14, 2023
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  5. fix genbank read error

    Keoni Gandall committed Sep 14, 2023
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  6. remove io.WriterTo checks

    Keoni Gandall committed Sep 14, 2023
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Commits on Sep 16, 2023

  1. fix with cmp.Equal

    Keoni Gandall committed Sep 16, 2023
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  2. Merge pull request #341 from TimothyStiles/slow5StreamVByte2 

    Add svb compression to slow5
    Koeng101 committed Sep 16, 2023
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Commits on Oct 28, 2023

  1. Merge branch 'main' into ioToBio

    Keoni Gandall committed Oct 28, 2023
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  2. genbank tests merged

    Keoni Gandall committed Oct 28, 2023
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  3. sample merge

    Keoni Gandall committed Oct 28, 2023
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  4. Merge branch 'main' of github.com:TimothyStiles/poly into ioToBio

    Keoni Gandall committed Oct 28, 2023
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  5. make linter happy

    Keoni Gandall committed Oct 28, 2023
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Commits on Oct 30, 2023

  1. Added generic collections module

    @abondrn
    abondrn committed Oct 30, 2023
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  2. Switched Feature.Attributes to use multimap

    @abondrn
    abondrn committed Oct 30, 2023
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  3. Fixed tests

    @abondrn
    abondrn committed Oct 30, 2023
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  4. Ran linter

    @abondrn
    abondrn committed Oct 30, 2023
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  5. Added copy methods

    @abondrn
    abondrn committed Oct 30, 2023
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  6. Adds new functional test that addresses case where there is a partial… 

    … on an implicit range, standardizes parse error format for clarity
    @abondrn
    abondrn committed Oct 30, 2023
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  7. Ran linter

    @abondrn
    abondrn committed Oct 30, 2023
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  8. Add capability to compute sequence features and marshal en masse

    @abondrn
    abondrn committed Oct 30, 2023
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  9. Add methods to convert polyjson -> genbank

    @abondrn
    abondrn committed Oct 30, 2023
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  10. Removed generic collections library in favor of hand-rolled multimap,… 

    … with the added benefit of better cmp interop
    @abondrn
    abondrn committed Oct 30, 2023
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  11. Propogate handrolled multimap to test files

    @abondrn
    abondrn committed Oct 30, 2023
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  12. Responded to more comments

    @abondrn
    abondrn committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. Reduced new example genbank file

    @abondrn
    abondrn committed Oct 31, 2023
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  2. Resolved lint errors, added test StoreFeatureSequences and fixed unco… 

    …vered bug
    @abondrn
    abondrn committed Oct 31, 2023
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  3. Added multimap.go file doc

    @abondrn
    abondrn committed Oct 31, 2023
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  4. Responded to more comments

    @abondrn
    abondrn committed Oct 31, 2023
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Commits on Nov 4, 2023

  1. First merge attempt

    @abondrn
    abondrn committed Nov 4, 2023
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  2. Fixed deref issue

    @abondrn
    abondrn committed Nov 4, 2023
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  3. Merged updated branch

    @abondrn
    abondrn committed Nov 4, 2023
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  4. Fixed tests, moved genbank files

    @abondrn
    abondrn committed Nov 4, 2023
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  5. Fixed fasta docs

    @abondrn
    abondrn committed Nov 4, 2023
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Commits on Nov 5, 2023

  1. Added changelog

    @abondrn
    abondrn committed Nov 5, 2023
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  2. Merge pull request #394 from abondrn/ioToBio-genbank 

    multimap implemented
    Koeng101 committed Nov 5, 2023
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Commits on Nov 10, 2023

  1. added to changelog

    Keoni Gandall committed Nov 10, 2023
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