v0.7.1

PopGenCore v0.7.1

• hotfix plink writer
  Diff since v0.7.0

v0.7.0

PopGenCore v0.7.0

Breaking changes

• allelematrix => matrix

Enhancements

• embrace the use of Val() for dispatch rather than if blocks
• Integrated plink (ped) file reading/writing
• write() has optional method omitting filename keyword
• baypass format file writer
• featurematrix added to make ML-compliant onehot encoded matrices

Diff since v0.6.0

v0.6.0

PopGenCore v0.6.0

Highlights

• A lot of basic code that gets used a lot is optimized and works a lot faster and allocates a lot less
  • examples include: ishom, uniquealleles, countalleles, allelefreq
• allelematrix code was migrated from PopGen.jl to *Core
• added baypass to file IO to write a Baypass input file. Baypass files cannot be read because there is no individual data in the matrix
• isbiallelic now allows monomorphic loci. This was a tough design call, but it made sense that "biallelic" can be interpreted as "at most two alleles"
• BUGFIX: genocount_expected now treats rearranged alleles as the same genotype (e.g. (1,2) == (2,1) and it didn't before)

Diff since v0.5.1

v0.5.1

PopGenCore v0.5.1

Diff since v0.5.0

v0.5.0

PopGenCore v0.5.0

Diff since v0.4.0

v0.4.0

PopGenCore v0.4.0

Diff since v0.3.0

v0.3.0

PopGenCore v0.3.0

Diff since v0.2.0

v0.2.0

PopGenCore v0.2.0

Diff since v0.1.1

Closed issues:

• [feature] overload getindex (#14)
• [bug] structure IO extremely slow for larger data (#10)
• [bug] write_to for structure format "filename" kwarg error (#11)

Merged pull requests:

• CompatHelper: add new compat entry for VariantCallFormat at version 0.5, (keep existing compat) (#12) (@github-actions[bot])
• CompatHelper: add new compat entry for CodecZlib at version 0.7, (keep existing compat) (#13) (@github-actions[bot])
• CompatHelper: bump compat for CSV to 0.9, (keep existing compat) (#15) (@github-actions[bot])

v0.1.1

PopGenCore v0.1.1

Diff since v0.1.0

Closed issues:

• [feature] meta df columns as direct objects of PooledArrays pools from loci df (#4) (not implemented)
• [feature] Rename meta and loci to metadata and genodata (#5)
• [feature] update PopData show (#6)

Merged pull requests:

• CompatHelper: add new compat entry for "StatsBase" at version "0.33" (#7) (@github-actions[bot])
• CompatHelper: add new compat entry for "StaticArrays" at version "1" (#8) (@github-actions[bot])

v0.1.0

PopGenCore v0.1.0

Closed issues:

• [bug] VCF header not found (#1)