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ChangeLog.md

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Changelog for cobot-io

[Unreleased]

[0.1.5.6] - 2024-12-18

  • Fix for gb-parser: spaces in name in LOCUS

[0.1.5.5] - 2024-05-16

  • Add 5ROX modification to Fasta parser.

[0.1.5.4] - 2024-05-16

  • Fix Fasta parser for unknown modifications on the end of the line.

[0.1.5.3] - 2023-12-08

  • Update tests and dependencies.

[0.1.5.2] - 2023-11-09

  • Add Ord for Fasta and related types.

[0.1.5.1] - 2023-01-17

  • Update dependencies for Haskell LTS-20.4.

[0.1.5.0] - 2022-09-30

Changed

  • Update FASTA parser to megaparsec.

[0.1.4.4] - 2022-06-02

Changed

  • Update more dependencies;
  • Fix new warnings in GHC-9.

[0.1.4.3] - 2022-03-23

Changed

  • Support GHC-9.2 packages in dependencies.

[0.1.4.2] - 2021-10-14

Changed

  • More types of multiline properties are supported.

[0.1.4.1] - 2021-10-07

Changed

  • CI fix

[0.1.4.0] - 2021-09-27

Changed

  • Redesigned the Range type to reflect all possible cases.
  • Switched to Megaparsec.

[0.1.3.25] - 2021-09-15

Added

  • Pedantic build and CI

[0.1.3.24] - 2021-09-10

Changed

  • GB parser made more verbose.

[0.1.3.23] - 2021-07-06

Added

Added ASN hydrogen names sometimes set by Scho

[0.1.3.22] - 2021-07-06

Changed

  • * -> Type for GHC-9.

[0.1.3.21] - 2021-07-03

Changed

  • Update dependency versions.

[0.1.3.20] - 2021-06-04

Changed

  • YLAB2-629: Fasta parser is now able to parse empty lines in the beginning.

[0.1.3.19] - 2021-04-30

Changed

  • Exports and instances for Biosset.

[0.1.3.18] - 2021-03-09

Fixed

  • Lowercase insertion code parsing in PDB.

[0.1.3.17] - 2021-02-18

Fixed

  • PDB parsing.

[0.1.3.16] - 2021-02-16

Fixed

  • Bad comment in GB parser.

[0.1.3.15] - 2021-02-16

Fixed

  • Unknown fields in GB.

[0.1.3.14] - 2021-02-10

Changed

  • Added ability to parse modifications in Fasta.

[0.1.3.13] - 2021-01-02

Changed

  • Allow QuickCheck-2.14.

[0.1.3.12] - 2020-11-11

Fixed

  • PDB parser error: it didn't account for segment identifier field.
  • Bond restoring in PDB for non-standard residue names.

[0.1.3.11] - 2020-11-08

Changed

  • Allow linear-0.21.

[0.1.3.10] - 2020-11-06

Fixed

  • SOURCE and ORIGIN in GB parser.

[0.1.3.9] - 2020-10-27

Fixed

  • FASTA parser can now parse empty lines with spaces.

[0.1.3.8] - 2020-10-22

Fixed

  • A couple of issues, that caused parametrization failures, fixed in bond restoring for PDB format.

[0.1.3.7] - 2020-10-14

Added

  • Generic fasta parser.

[0.1.3.6] - 2020-07-14

Added

  • Convertation from Models to PDB.
  • Writer for PDB.
  • renameChains function that renames chains in a model.

[0.1.3.5] - 2020-05-26

Fixed

  • Correctly clean BasecalledSequenceWithRawData, including inner quality.

[0.1.3.4] - 2020-05-14

Added

  • instance Cleanable BasecalledSequenceWithRawData.

[0.1.3.3] - 2020-05-07

Added

  • Type and decoder for ab1 with raw channel data and peak locations.

Fixed

  • Use supplied thresholds instead of default ones in the implementation of cleanWith;
  • Do not run IO in hspec Spec monad, use beforeAll.

[0.1.3.2] - 2020-04-15

Changed

  • Resolver version up.
  • Moving from less-wrong to biocad.

[0.1.3.1] - 2020-04-02

Fixed

  • Reading of insertion code for residues in MAE.

[0.1.3.0] - 2020-03-27

Added

  • Residue index in Structure.
  • Atom input index in Structure.
  • Bond restoring for PDB.
  • Tests for PDB -> Model conversion.

Changed

  • GlobalID now 0-based in mae, PDB, and MMTF.

Fixed

  • A lot of things.

[0.1.2.10] - 2020-03-27

Added

  • Lenses for Structure.

[0.1.2.9] - 2020-03-12

Added

  • Function filterAtomsOfModel to filter atoms of model by the given predicate.

Fixed

  • Grouping by residues when converting Mae to Model.

[0.1.2.8] - 2020-03-12

Added

  • instance Traversable (Sequence mk w).

[0.1.2.7] - 2020-02-11

Changed

  • Support GHC-8.8.

[0.1.2.6] - 2019-12-12

Fixed

  • Fixes for instance of StructureModels for Mae when working with structures without explicit chain names.

[0.1.2.5] - 2019-12-24

Fixed

  • Possibility to have spaces in Fasta sequences.

[0.1.2.4] - 2019-12-23

Added

  • Preprocessing for pdb-files.
  • Pdb parser.

[0.1.2.3] - 2019-12-12

Fixed

  • Fixes for .mae pasrser.
  • Fixes for instance of StructureModels for Mae.

[0.1.2.2] - 2019-11-27

Added

  • Instance of StructureModels for Mae.

Fixed

  • Fix for .mae pasrser.

[0.1.2.1] - 2019-11-25

Added

  • Parser for MAE.

[0.1.2.0] - 2019-09-03

Added

  • Parser for FASTA.
  • Writer for FASTA.

[0.1.1.1] - 2019-06-05

Changed

  • length on Sequence now works in O(1).

[0.1.1.0] - 2019-05-13

Added

  • New version of module Bio.Sequence hat introduces IsSequence type class and Sequence datatype.
  • Type GenBankSequence describing structure of .gb file.
  • Parser for GenBankSequence.
  • Writer for GenBankSequence.

Changed

  • ABI cleaner and decoder now work with type ABIRaw.

[0.1.0.1] - 2019-02-28

Added

  • Field chemCompType in Residue.

Fixed

  • codec10.