ska - Release v0.4.0 (ska lo)

This release adds the ska lo command for detection of nearby SNPs and indels.

What's Changed

• Added link & reference to the sandbox.bio tutorial. by @vrbouza in https://github.com/bacpop/ska.rust/pull/88
• Covbuildmerge by @jhellewell14 in https://github.com/bacpop/ska.rust/pull/89
• Skalo by @jhellewell14 in https://github.com/bacpop/ska.rust/pull/86
• updated skalo with indel output by @rderelle in https://github.com/bacpop/ska.rust/pull/91

New Contributors

• @vrbouza made their first contribution in https://github.com/bacpop/ska.rust/pull/88
• @jhellewell14 made their first contribution in https://github.com/bacpop/ska.rust/pull/89
• @rderelle made their first contribution in https://github.com/bacpop/ska.rust/pull/91

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.11...v0.4.0

- Rust
Published by github-actions[bot] about 1 year ago

ska - Release v0.3.11

What's Changed

• Better default filtering options for ska distance by @johnlees in https://github.com/bacpop/ska.rust/pull/82

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.10...v0.3.11

- Rust
Published by johnlees over 1 year ago

ska - Release v0.3.10

What's Changed

• ska delete upgrade by @johnlees in https://github.com/bacpop/ska.rust/pull/80

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.9...v0.3.10

- Rust
Published by github-actions[bot] over 1 year ago

ska - Release v0.3.9

What's Changed

• Fix for ska cov with low counts by @johnlees in https://github.com/bacpop/ska.rust/pull/76

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.8...v0.3.9

- Rust
Published by github-actions[bot] over 1 year ago

ska - Release v0.3.8

What's Changed

• Adding max frequence reads parameter by @apollis44 in https://github.com/bacpop/ska.rust/pull/74
• Simplified proportion reads computation by @apollis44 in https://github.com/bacpop/ska.rust/pull/75

New Contributors

• @apollis44 made their first contribution in https://github.com/bacpop/ska.rust/pull/74

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.7...v0.3.8

- Rust
Published by github-actions[bot] over 1 year ago

ska - Release v0.3.7

What's Changed

• Consistent method for dealing with ref bias in ska map by @johnlees in https://github.com/bacpop/ska.rust/pull/70

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.6...v0.3.7

- Rust
Published by github-actions[bot] almost 2 years ago

ska - Release v0.3.6

What's Changed

• Fix double file prefix; update VCF parsing by @johnlees in https://github.com/bacpop/ska.rust/pull/66

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.5...v0.3.6

- Rust
Published by github-actions[bot] about 2 years ago

ska - Release v0.3.5

What's Changed

• Filter tweaks by @johnlees in https://github.com/bacpop/ska.rust/pull/63

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.4...v0.3.5

- Rust
Published by github-actions[bot] about 2 years ago

ska - Release v0.3.4

What's Changed

• 0.3.4 candidate -- final feature requests by @johnlees in https://github.com/bacpop/ska.rust/pull/61

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.3...v0.3.4

- Rust
Published by github-actions[bot] over 2 years ago

ska - Release v0.3.3

What's Changed

• Add optional output filename option -o to ska weed. by @tmaklin in https://github.com/bacpop/ska.rust/pull/55
• Fix for ska delete by @johnlees in https://github.com/bacpop/ska.rust/pull/58
• Fix for multi-contig references in map by @johnlees in https://github.com/bacpop/ska.rust/pull/60

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.2...v0.3.3

- Rust
Published by github-actions[bot] over 2 years ago

ska - Release v0.3.2

What's Changed

• Fix for multicopy palindromes by @johnlees in https://github.com/bacpop/ska.rust/pull/49

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.1...v0.3.2

- Rust
Published by github-actions[bot] over 2 years ago

ska - Release v0.3.1

What's Changed

• Add k-mer counts per sample to ska nk; efficiency of dup counting by @johnlees in https://github.com/bacpop/ska.rust/pull/40
• Enchanced filtering options by @johnlees in https://github.com/bacpop/ska.rust/pull/44
• Restore filter accuracy for fastq input by @johnlees in https://github.com/bacpop/ska.rust/pull/46

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.3.0...v0.3.1

- Rust
Published by github-actions[bot] over 2 years ago

ska - Release v0.3.0

What's Changed

• Deal with palindromes by @johnlees in https://github.com/bacpop/ska.rust/pull/30
• Fix ambiguous bases in pseudoalignment by @johnlees in https://github.com/bacpop/ska.rust/pull/31
• Fix filtering option name in documentation. by @tmaklin in https://github.com/bacpop/ska.rust/pull/33
• Add mode to automatically determine a count cutoff by @johnlees in https://github.com/bacpop/ska.rust/pull/34
• Add ska distance, and clustering script by @johnlees in https://github.com/bacpop/ska.rust/pull/35
• Add NJ trees to clustering script by @johnlees in https://github.com/bacpop/ska.rust/pull/36
• Mask repeats with Ns during ska map by @johnlees in https://github.com/bacpop/ska.rust/pull/37

New Contributors

• @tmaklin made their first contribution in https://github.com/bacpop/ska.rust/pull/33

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.2.4...v0.3.0

- Rust
Published by github-actions[bot] over 2 years ago

ska - Release v0.2.4

What's Changed

• Add 'reverse' weed to keep only selected split k-mers by @johnlees in https://github.com/bacpop/ska.rust/pull/24

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.2.3...v0.2.4

- Rust
Published by github-actions[bot] almost 3 years ago

ska - Release v0.2.3

What's Changed

• Faster filter for reads by @johnlees in https://github.com/bacpop/ska.rust/pull/20
• Move test dependencies to test only by @johnlees in https://github.com/bacpop/ska.rust/pull/21

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.2.2...v0.2.3

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.2.2

What's Changed

• Memory optimisation: don't store whole build array by @johnlees in https://github.com/bacpop/ska.rust/pull/19

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.2.1...v0.2.2

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.2.1

What's Changed

• README update by @johnlees in https://github.com/bacpop/ska.rust/pull/15
• Add more types of quality score filtering by @johnlees in https://github.com/bacpop/ska.rust/pull/16

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.2.0...v0.2.1

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.2.0

What's Changed

• Replace hashes with nthash by @johnlees in https://github.com/bacpop/ska.rust/pull/14
• Add support for up to k=63 using u128 by @johnlees in https://github.com/bacpop/ska.rust/pull/13

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.1.2...v0.2.0

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.1.2

What's Changed

• Add middle base to read count filtering by @johnlees in https://github.com/bacpop/ska.rust/pull/10
• Add a test of version number increase to gha by @johnlees in https://github.com/bacpop/ska.rust/pull/11
• Actually need to remove second version check on tag push by @johnlees in https://github.com/bacpop/ska.rust/pull/12

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.1.1...v0.1.2

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.1.1

What's Changed

• Add actions to automate release by @johnlees in https://github.com/bacpop/ska.rust/pull/3
• Try adding codecov by @johnlees in https://github.com/bacpop/ska.rust/pull/6
• Add logo to readme by @johnlees in https://github.com/bacpop/ska.rust/pull/8
• Add more alignment filtering options by @johnlees in https://github.com/bacpop/ska.rust/pull/9

Full Changelog: https://github.com/bacpop/ska.rust/compare/v0.1.0...v0.1.1

- Rust
Published by github-actions[bot] about 3 years ago

ska - Release v0.1.0

What's Changed

• Try clippy gha by @johnlees in https://github.com/bacpop/ska.rust/pull/1
• Redo the alignment writer for ska map by @johnlees in https://github.com/bacpop/ska.rust/pull/2

New Contributors

• @johnlees made their first contribution in https://github.com/bacpop/ska.rust/pull/1

Full Changelog: https://github.com/bacpop/ska.rust/commits/v0.1.0

- Rust
Published by github-actions[bot] about 3 years ago