Version 0.9.0 - Githubissues

PlantandFoodResearch / MCHap

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

MIT License

18 stars 3 forks source link

Version 0.9.0 #169

Closed timothymillar closed 10 months ago

timothymillar commented 10 months ago

New Features:

Added tool mchap find-snvs to generate a template VCF for assembly #166
Option to report posterior probability of allele occurrence #162
Added generic option to filter input haplotypes #168

Bug Fixes:

Allow samples with multiple read groups #164
Correct number of cores used when specifying multiple cores #150
Simplify specification of prior allele frequencies #154
Improve performance when working with CRAM files #167

CLI Changes:

Added mchap find-snvs tool #166
Added optional --reference argument to call and call-exact tools #167
Replaced --skip-rare-haplotypes argument with --filter-input-haplotypes #168
Replaced --haplotype-frequencies and --haplotype-frequencies-prior with --prior-frequencies #154

VCF Changes:

Added AOP field to record posterior probability of an allele occurring at any copy number #162

Internal Changes:

Changes to using multiple process to minimize file handel creation #167
Added pandas as a dependency