Code

Io to bio#1

Code

Merged

Koeng101 merged 70 commits intomainKoeng101/dnadesign:mainfrom ioToBioKoeng101/dnadesign:ioToBioCopy head branch name to clipboardDec 7, 2023

+3,030-2,190

Commits

Commits on Aug 24, 2023

• Moved io to bio

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  b87947b

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• fixed io imports

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Commits on Aug 31, 2023

• Add more generic definitions to bio

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Commits on Sep 1, 2023

• Update bio/fastq/fastq.go

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• update fasta

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• Merge branch 'ioToBio' of github.com:TimothyStiles/poly into ioToBio

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• add fasta updates and parser

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Commits on Sep 2, 2023

• made readability improvements

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• changed ParseWithHeader

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• removed int64 in reads

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• add more example tests

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• gotta update this for this tests!

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Commits on Sep 5, 2023

• integrate slow5

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• have examples covering most of changes

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• removed interfaces

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Commits on Sep 7, 2023

• updated with NewXXXParser

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• added 3 parsers

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• added pileup

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Commits on Sep 9, 2023

• add concurrent functions plus better documentation

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Commits on Sep 11, 2023

• moved svb to ioToBio

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• Improve tests

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• make better docs for header

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Commits on Sep 12, 2023

• Update bio/fasta/fasta_test.go

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• changed name of LowLevelParser to parserInterface

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• Merge branch 'main' into ioToBio

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• zw -> zipWriter

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• remove a identifier from pileup

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Commits on Sep 13, 2023

• genbank parser now compatible

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• writeTo interface now fulfilled

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• make linter happy :)

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Commits on Sep 14, 2023

• convert all types to io.WriterTo

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• fixed linter issues

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• handle EOF better

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  4b50625

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• fixed tutorial

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• fix genbank read error

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• remove io.WriterTo checks

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Commits on Sep 16, 2023

• fix with cmp.Equal

  Koeng101

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• Merge pull request #341 from TimothyStiles/slow5StreamVByte2

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Commits on Oct 28, 2023

• Merge branch 'main' into ioToBio

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• genbank tests merged

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• sample merge

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• Merge branch 'main' of github.com:TimothyStiles/poly into ioToBio

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• make linter happy

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Commits on Oct 30, 2023

• Added generic collections module

  abondrn

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• Switched Feature.Attributes to use multimap

  abondrn

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• Fixed tests

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• Ran linter

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• Added copy methods

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• Adds new functional test that addresses case where there is a partial on an implicit range, standardizes parse error format for clarity

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• Ran linter

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• Add capability to compute sequence features and marshal en masse

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• Add methods to convert polyjson -> genbank

  abondrn

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• Removed generic collections library in favor of hand-rolled multimap, with the added benefit of better cmp interop

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• Propogate handrolled multimap to test files

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• Responded to more comments

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Commits on Oct 31, 2023

• Reduced new example genbank file

  abondrn

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• Resolved lint errors, added test StoreFeatureSequences and fixed uncovered bug

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• Added multimap.go file doc

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• Responded to more comments

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Commits on Nov 4, 2023

• First merge attempt

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• Fixed deref issue

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• Merged updated branch

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• Fixed tests, moved genbank files

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• Fixed fasta docs

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Commits on Nov 5, 2023

• Added changelog

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• Merge pull request #394 from abondrn/ioToBio-genbank

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Commits on Nov 10, 2023

• added to changelog

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Commits on Dec 7, 2023

• changed

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  8fb83b8

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• Merge branch 'main' into ioToBio

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• fix linter issues

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