Changelog for cobot-io

[Unreleased]

[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.