Changelog for cobot-io

[Unreleased]

[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.