v4.1.6

• Fixes slowness loading reference panels with mixed ploidy across samples.
• Adds --min-block-size, --max-block-size, and --slope-unit.

v4.1.5

• Increases default --min-ratio to 1e-4.
• Adds --min-ratio-behavior option to allow for skipping chunks with low number of target sites.
• Improves accuracy by applying --min-recom to reference sites instead of typed sites.

v4.1.4

• Fixes bug that produced incorrect ploidy for target VCFs that contained mixed ploidy (e.g., chromosome X) and had sample sizes larger than --temp-buffer (#61).

v4.1.3

• Updates documention in README
• Improves output format detection from file extension
• Adds --decay option
• Corrections in output VCF headers
• Updates binary packaging to use musl
• Adds man page target
• Adds cmake-only alternative to cget
• Adds --temp-prefix option

v4.1.2

• Adds support for reference panels that contain both haploid and diploid samples
• Adds make test

v4.1.1

• Fixes empty block error when compressing reference.
• Backwards compatability fixes for command line args.
• Mean-imputes variants that are exclusive to target file.
• Carries over ID column from reference panel.
• Allows for missing values in target file.

v4.1.0

This version is NOT backwards compatible. Reference panel must be upgraded to new format with minimac4 --update-m3vcf old.m3vcf.gz > new.msav.

Updates:

• Memory optimizations
• Speed optimizations
• Subsetting of reference panel samples
• Random access to genomic regions
• Support for BCF and SAV file formats

v1.0.3 (a.k.a. v4.0.3)

• Changes LDS format from string to number
• Changes delimiter for LDS from vertical slash to comma
• Defaults to release build when CMAKE_BUILD_TYPE is not passed.
• Fixes negative probability bug
• Fixes bug in computing switch probabilities
• Fixes crash when number of temporary files exceed ulimit
• Fixes broken zlib URL

v1.0.2

Bumps version to 1.0.2

v1.0.0

Initial release.