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Beta v0.10.0#184

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timothymillar merged 84 commits intoPlantandFoodResearch:masterPlantandFoodResearch/MCHap:masterfrom timothymillar:atomizetimothymillar/MCHap:atomizeCopy head branch name to clipboardSep 18, 2024

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Commits

Commits on May 8, 2024

• Use scm for versioning and -v to get version PlantandFoodResearch#179

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Commits on May 9, 2024

• Add more optional --report fields PlantandFoodResearch#174

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Commits on May 10, 2024

• Improve handeling of INFO and FORMAT fields

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• Add UAN and MCI INFO fields

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• Rename fields PHQ and PHPM to SQ and SPM

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• Test AOPSUM with AOP

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• Test SNVDP optional field

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• Add tests for optional ACP fields

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• Update CLI help text

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Commits on May 12, 2024

• Update docs

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• Update example

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Commits on May 13, 2024

• Changelog

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Commits on Jul 9, 2024

• Initial pedigree submodule

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• Correct PMF for second gamete of unknown origin

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• Docstrings

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• Rename pedigree sampler and add docstring

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• Ensure zero-count reads removed from likelihood function

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• Introduce H-K lambda parameter for diploid gametes

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• Tests

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• Tests for log_gamete_pmf

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• Test second_gamete_log_pmf

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• Reorder test perms

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• Initial PedigreeCallingMCMC class

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• Initial call-pedigree CLI

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• Report pedigree posterior error PEDERR

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• Test pedigree validation

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• Improve ploidy and inbreeding handeling with pedigree

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• Note to handle read io for dummy samples

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• Seperate out mh-probabilities function

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• Simplify use of lambda in gamete PMF

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• Add gamete_allele_log_pmf

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• Fix pedigree MH step proposal ratios

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• WIP pedigree gibbs step

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• Fix gibbs prior

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• fixup

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• assume unknown gametes are outcrossed

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• Add Gibbs option to pedigree MCMC

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• Fix tests for pedigree prior

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• Update call_pedigree for arg changes in main

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• Handle samples with no alignmentfiles

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• Fix whitespace

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• Fix bug in log_unknown_const_prior

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• Correct markov_blanket_log_allele_probability

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• Improve testing of pedigree prior

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• Add test for gamete_const_log_pmf

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• Handel edge cases

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• Document details of trio_allele_log_pmf

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• Add more pedigree trantion probabilities functions

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• Test for PedigreeCallingMCMC

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• Allow prior on frequencies in pedigree calling

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• Clean up call application handeling of prior freqs

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• Pass prior freqs to pedigree calling application

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• Tests for PedigreeAllelesMultiTrace

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• Remove unsupported inbreeding argument from call-pedigree

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• Add experimental warning to call-pedigree

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• Tests for mchap call-pedigree cli

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• Use sample_children matrix

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• Cache smaller combinatorial values

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• Reuse dosage arrays in pedigree mcmc

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• Update pedigree prio docstrings and tests

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• Use a scratch array for dosage allele freqs

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• Initial implimentation of parental allele swap step

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• Fixup after rebase on 0.9.1

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• Bump version in test VCFs

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• Change default for --gamete-error to 0.01

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• Bump version in test VCFs

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• Add draft call-pedigree tutorial

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• Update setup.py

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• Add call-pedigree branch to CI testing

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• Force formating with black

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Commits on Jul 10, 2024

• Rebase call-pedigree on master

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• Test new optional fields for call-pedigree

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• Minor fixes for numpy2

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• Pin numpy to 1.x numpy/numpy#26898

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• Add atomize application

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• Tests for atomize tool

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• Add INFO AC, ACP and DP fields to atomize

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• Update tests for atomize

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• Additional tests for atomize

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Commits on Sep 10, 2024

• Update examples

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• Mark atomize as experimental

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• Update changelog

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• Run pre-commit on cli.py

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Commits on Sep 18, 2024

• Flag experimental tools in readme

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