Version 0.5.0 - Githubissues

PlantandFoodResearch / MCHap

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

MIT License

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Version 0.5.0 #112

Closed timothymillar closed 3 years ago

timothymillar commented 3 years ago

New features:

Added Gibbs sampler re-calling tool: mchap call #110, #104
Added exact re-calling tool:mchap call-exact #110

Changes to CLI:

Removed exact re-calling option from mchap assemble #110
Reordering of some CLI arguments to facilitate reusing arguments between sub-tools

Internal changes:

Move CLI parser arguments into reusable components
Reuse CLI tool methods via inheritance
Prior and likelihood functions for known sets of haplotypes
Generate Locus objects from pysam variant records
Reorganize internal sub-modules