v1.1.0

HapLink v1.1.0

Diff since v1.0.0

Merged pull requests:

• chore: Downgrade FASTX compat to v1 (#56) (@MillironX)
• perf: Use sparse matrices for haplotype calling (#60) (@MillironX)
• perf: Add bounds for haplotype matrix (#61) (@MillironX)
• docs: Polish docs (#62) (@MillironX)
• Release v1.1.0 (#63) (@MillironX)

Closed issues:

• [Feature]: Add to Bioconda (#39)

v1.0.0

HapLink v1.0.0

Diff since v0.7.1

Closed issues:

• Feature: Implement in pure Julia (#24)
• Feature: Add option to keep filtered variants in VCF output (#28)
• Feature: Use Commonicon.jl for CLI (#38)
• Feature: Separate raw and ml haplotype calling into separate commands (#40)
• Feature: Add Nix configuration (#41)
• Feature: Add Earthfile for testing and docs (#42)
• [Bug]: Add haplink sequences command back (#43)

Merged pull requests:

• Feature/sequence variation.jl rewrite (#35) (@MillironX)
• Replace Husky with pre-commit (#36) (@MillironX)
• [FIX]: Correct calculations for linkage disequilibrium and Chi-squared test (#37) (@MillironX)
• feat: Add Earthfile for documentation builds (#45) (@MillironX)
• fix: Add haplink sequences back into CLI (#46) (@MillironX)
• Implement Comonicon.jl interface (#48) (@MillironX)
• Only output simulation settings when using simulated reads (#49) (@MillironX)
• CompatHelper: add new compat entry for Comonicon at version 1, (keep existing compat) (#50) (@github-actions[bot])
• Docs (#52) (@MillironX)
• feat: Add Nix config (#53) (@MillironX)
• Release v1.0.0 (#54) (@MillironX)

v0.7.1

Fixed

• VCF output files no longer contain invalid characters (#30)

v0.7.0: Update tag finding function in CI

Fixed

• The CI scripts have been fixed

v0.5.1: Version bump to 0.5.1

Signed-off-by: Thomas A. Christensen II <[email protected]>

Version bump to v0.5.0

Signed-off-by: Thomas A. Christensen II <[email protected]>

v0.4.1: Version bump

Signed-off-by: Thomas A. Christensen II <[email protected]>

v0.3.0: Correct tag name

Signed-off-by: Thomas A. Christensen II <[email protected]>

v0.2.0

Update Dockerfile

Signed-off-by: Thomas A. Christensen II <[email protected]>

v0.1.2

Bump version number

Signed-off-by: Thomas A. Christensen II <[email protected]>