0.0.8

What's Changed

• Remove requiring the first value of input recombination probability array be zero by @szhan in #138
• Allow for invariant sites in input data by @szhan in #139

Full Changelog: v0.0.7...v0.0.8

0.0.7

Summary of changes

• The num_alleles argument is removed from the main API functions, and ploidy is added as a required argument.
• When using the diploid algorithms (i.e. ploidy set to 2), the input query is a sequence of unphased genotypes instead of a pair of haplotypes.
• Simulation parameters are tweaked so that the test haplotypes meet certain criteria (e.g. enough variable sites).

Full Changelog: v0.0.6...v0.0.7

0.0.6

Summary of changes:

• Added support for NONCOPY values representing non-copiable states in reference haplotypes.
• Refactored the source code extensively, from the API functions to tests.
• Improved test coverage for both the haploid and diploid LS HMM implementations.
• Added or improved documentation throughout.
• Drafted a README (mainly explaining the haploid LS HMM).
• Added a Jupyter notebook to show how to use the main API functions for the haploid case.

0.0.5

Added multi-allelic support and testing in the haploid case, removed redundant modules.

0.0.4

Added missingness to the LS algorithm

0.0.2

Cleaned up API, added path ll calculation.

Initial alpha for resting

Merge pull request #10 from jeromekelleher/ready-for-release

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