Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

3.1.0 - 2023-01-03

Added

Grantham's substitution matrix (#88)

3.0.0 - 2022-10-08

Added

Alignment position support (#44)
Support for P CIGAR operation (#64)

Fixed

Hard clips no longer consume bases (#64)

2.3.0 - 2022-10-01

Added

Getter functions for AlignedSequence, PairwiseAlignment, and PairwiseAlignmentResult (#83)

2.2.0 - 2022-07-07

Added- Compact printing of alignments (#53)

More SubstitutionMatrix operations (#60)
Downstream tests (#70)
SSH secret to TagBot.yml (#71)- Doctests as part of the unit tests (#78)

Changed- Updated chat links (#ebea200c)

Expanded test matrix, adding julia v1.6 (#77)
Incremented BioSequences compatibility to v3 (#72)
Incremented BioSymbols compatibility to v5 (#72)
Adjusted test matrix for minimum compatibility (#72)
Updated doctests (#72)

Removed

❗ Removed Gitter chat links (#ebea200c)
❗ Dropped support for julia less than v1.6 (#72)
❗ Removed alignment position support, as it was a breaking change (#44, #76)

Fixed

Doctests (#78)

2.1.0 - 2022-02-10 [YANKED]

Added

Zenodo badge (#c49bb0a3)

Removed

❗ Dropped support for julia less than v1 (#50)

Changed

2.0.1 - 2022-02-08 [UNREGISTERED]

Added

Alignment position support (#44)

Changed

Updated CI to use GitHub actions (#47)
master set as the main development branch (#49, #50)

Removed

❗ Reverted the use of BioJulia registry, the package switched to General Julia Registry (#48)

2.0.0

Added

BioJulia registry.

Changed

Migrated from BioCore to BioGenerics.
Updated to use BioSequences v2.
Updated CI.

Removed

❗ BAM and SAM submodules were moved to XAM.jl.
❗ Support for julia v0.7 and v1.0 was dropped.

1.0.1 - 2020-01-24

Added

Support for julia v1.1, v1.2, and v1.3.

Changed

Updated CI.

Fixed

Function convert(BAM.Record, x::Vector{UInt8} updated to Julia v. 1.0. (#23)
haskey(x::BAM.Record, y::String). (#24)
Reading BAM files from processes. (#29)
Use @info instead of info. (#36)

1.0.0 - 2018-09-18

Added

Support for julia v0.7 / v1.0.

Removed

❗ Support for julia v0.6 has been dropped.

0.3.0 - 2018-06-15

Added

Contributing files were added to this project.
A method called BAM.ispositivestrand is added to test for the relevant flag in BAM records. Thanks @phaverty 😄
Support for records with CIGAR strings with >65535 op-codes has been added.

Changed

Documentation has been updated and uses the Documenter.jl native html generator.

0.2.0 - 2017-08-01

Dependencies

❗ Support for julia v0.5 has been dropped.
❗ Some dependency lower bound requirements were adjusted for Automa, BGZFStreams, BioSequences, and IntervalTrees.

0.1.0 - 2017-06-30

This initial release extracted the alignment utilities out from Bio.jl into this dedicated package.