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io->bio#339

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Koeng101 wants to merge 67 commits intomainbebop/poly:mainfrom ioToBiobebop/poly:ioToBioCopy head branch name to clipboard

+2,715-2,147

Commits

Commits on Aug 24, 2023

• Moved io to bio

  

  Keoni Gandall

  committed
  b87947b

• fixed io imports

  

  Keoni Gandall

  committed
  5c887a3

Commits on Aug 31, 2023

• Add more generic definitions to bio

  

  Keoni Gandall

  committed
  d8f4b38

Commits on Sep 1, 2023

• Update bio/fastq/fastq.go

  Show description for 4fb41ff
  

  Koeng101

  and

  carreter

  authored
  4fb41ff

• update fasta

  

  Keoni Gandall

  committed
  2452282

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

  

  Keoni Gandall

  committed
  6dda2b9

• add fasta updates and parser

  

  Keoni Gandall

  committed
  16fbcbd

Commits on Sep 2, 2023

• made readability improvements

  

  Keoni Gandall

  committed
  382a014

• changed ParseWithHeader

  

  Keoni Gandall

  committed
  0bbd05e

• removed int64 in reads

  

  Keoni Gandall

  committed
  eb68f81

• add more example tests

  

  Keoni Gandall

  committed
  344220c

• gotta update this for this tests!

  

  Keoni Gandall

  committed
  03f8b68

Commits on Sep 5, 2023

• integrate slow5

  

  Keoni Gandall

  committed
  6199c43

• have examples covering most of changes

  

  Keoni Gandall

  committed
  65f0539

• removed interfaces

  

  Keoni Gandall

  committed
  8ff6da4

Commits on Sep 7, 2023

• updated with NewXXXParser

  

  Keoni Gandall

  committed
  00732a4

• added 3 parsers

  

  Keoni Gandall

  committed
  3ce8109

• added pileup

  

  Keoni Gandall

  committed
  630bd88

Commits on Sep 9, 2023

• add concurrent functions plus better documentation

  

  Keoni Gandall

  committed
  df98fe3

Commits on Sep 11, 2023

• moved svb to ioToBio

  

  Keoni Gandall

  committed
  fa4d29a

• Improve tests

  

  Keoni Gandall

  committed
  f80b317

• make better docs for header

  

  Keoni Gandall

  committed
  37859a8

Commits on Sep 12, 2023

• Update bio/fasta/fasta_test.go

  Show description for e24801b
  

  Koeng101

  and

  carreter

  authored
  e24801b

• changed name of LowLevelParser to parserInterface

  

  Keoni Gandall

  committed
  584b73e

• Merge branch 'main' into ioToBio

  

  Keoni Gandall

  committed
  da7118a

• zw -> zipWriter

  

  Keoni Gandall

  committed
  5e6204f

• remove a identifier from pileup

  

  Keoni Gandall

  committed
  90316d3

Commits on Sep 13, 2023

• genbank parser now compatible

  

  Keoni Gandall

  committed
  7b2cd52

• writeTo interface now fulfilled

  

  Keoni Gandall

  committed
  9b55fda

• make linter happy :)

  

  Keoni Gandall

  committed
  6655565

Commits on Sep 14, 2023

• convert all types to io.WriterTo

  

  Keoni Gandall

  committed
  11972ae

• fixed linter issues

  

  Keoni Gandall

  committed
  12a4b48

• handle EOF better

  

  Keoni Gandall

  committed
  4b50625

• fixed tutorial

  

  Keoni Gandall

  committed
  f44721c

• fix genbank read error

  

  Keoni Gandall

  committed
  b192fda

• remove io.WriterTo checks

  

  Keoni Gandall

  committed
  3eab1f9

Commits on Sep 16, 2023

• fix with cmp.Equal

  

  Keoni Gandall

  committed
  0edfd1c

• Merge pull request #341 from TimothyStiles/slow5StreamVByte2

  Show description for 34de749
  

  Koeng101

  authored
  34de749

Commits on Oct 28, 2023

• Merge branch 'main' into ioToBio

  

  Keoni Gandall

  committed
  6abe0cd

• genbank tests merged

  

  Keoni Gandall

  committed
  4c61c22

• sample merge

  

  Keoni Gandall

  committed
  1d23668

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

  

  Keoni Gandall

  committed
  56772bb

• make linter happy

  

  Keoni Gandall

  committed
  956d26e

Commits on Oct 30, 2023

• Added generic collections module

  abondrn

  committed
  158fcf1

• Switched Feature.Attributes to use multimap

  abondrn

  committed
  8862a6c

• Fixed tests

  abondrn

  committed
  ef07e94

• Ran linter

  abondrn

  committed
  cac1e55

• Added copy methods

  abondrn

  committed
  8025bc2

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

  abondrn

  committed
  1f49f9d

• Ran linter

  abondrn

  committed
  8112866

• Add capability to compute sequence features and marshal en masse

  abondrn

  committed
  fec8796

• Add methods to convert polyjson -> genbank

  abondrn

  committed
  9ce9f4f

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

  abondrn

  committed
  89a2ba4

• Propogate handrolled multimap to test files

  abondrn

  committed
  b88d7b8

• Responded to more comments

  abondrn

  committed
  b4c3a37

Commits on Oct 31, 2023

• Reduced new example genbank file

  abondrn

  committed
  8b82d7b

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

  abondrn

  committed
  f523651

• Added multimap.go file doc

  abondrn

  committed
  1270ec8

• Responded to more comments

  abondrn

  committed
  9c322f6

Commits on Nov 4, 2023

• First merge attempt

  abondrn

  committed
  f124fae

• Fixed deref issue

  abondrn

  committed
  98b6984

• Merged updated branch

  abondrn

  committed
  fc2ca75

• Fixed tests, moved genbank files

  abondrn

  committed
  25e0f61

• Fixed fasta docs

  abondrn

  committed
  60abf6d

Commits on Nov 5, 2023

• Added changelog

  abondrn

  committed
  7e3c812

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

  Show description for 35a5492
  

  Koeng101

  authored
  35a5492

Commits on Nov 10, 2023

• added to changelog

  

  Keoni Gandall

  committed
  433df00