v0.3.0

Intro

In this release, the FastAPI API for AutoACMG package was introduced. Now it's even simpler to use AutoACMG!

What's Changed

• Provide an API for AutoACMG by @gromdimon in #216
• Dockerize the application by @gromdimon in #218
• New usage docs by @gromdimon in #219
• Update comparison_criteria_custom.csv by @gromdimon in #221
• Update usage page in documentation by @gromdimon in #222
• Fix docker related CI workflows by @gromdimon in #223

Full Changelog: v.0.2.0...v0.3.0

v.0.2.0

Intro

In this releaase custom VCEP rules from ClinGen were implemented and integrated into AutoACMG algorithm. Some additional minor fixes and features were also included.

What's Changed

• Add vcr.py for end-to-end tests by @gromdimon in #158
• Refactor codebase for better internal data structure by @gromdimon in #159
• Update .gitattributes by removing \ by @gromdimon in #165
• Increase test coverage by @gromdimon in #162
• Fix readme by @gromdimon in #166
• 161 add detailed description on dev quickstart by @gromdimon in #167
• Implement some VCEPs for PM1 criterion by @gromdimon in #169
• Implement pm1 vcep rules by @gromdimon in #171
• Implement BP7 VCEP rules by @gromdimon in #173
• PM4 and BP3 rules for VCEPs by @gromdimon in #177
• Implement PP2 and BP1 VCEP rules by @gromdimon in #182
• Add VCEP specifications by @gromdimon in #184
• Implement pm2, ba1, bs1 rules by @gromdimon in #186
• Implement custom Not applicable VCEP rules for PVS1 by @gromdimon in #187
• Implement full gene deletion method by @gromdimon in #188
• Implement del_disrupt_rf method by @gromdimon in #189
• Implemente undergo_nmd method by @gromdimon in #190
• Implement "In biologically relevant transcript" method for strucvars by @gromdimon in #191
• Implement VCEPs for PS1 and PM5 by @gromdimon in #192
• Implement custom PP3 and BP4 rules by @gromdimon in #196
• Add VCEP Documentation by @gromdimon in #199
• Implement crit4prot function for stucvars by @gromdimon in #201
• Implement lof is frequent in population for strucvars by @gromdimon in #202
• Implement lof removes more than 10% of protein for strucvars by @gromdimon in #203
• Implement duplication - tandem setting to temporary fix the PVS1 criteria for duplication CNVs by @gromdimon in #205
• Add misZ score evaluation for PP2 and BP1 by @gromdimon in #207
• Rename Notmet and Met prediction statuses by @gromdimon in #208
• Optimize tests by @gromdimon in #209
• Fix failing tests in PM2 by @gromdimon in #210
• Update documentation by @gromdimon in #214

Full Changelog: v.0.1.0...v.0.2.0

v.0.1.0

First initial release

• Update README.md by @gromdimon in #12
• Update PULL_REQUEST_TEMPLATE.md by @gromdimon in #13
• Fix Autodocumentation on readthedocs by @gromdimon in #14
• Replace conf.py by @gromdimon in #16
• Implement pydantic models validation for JSON outputs from APIs by @gromdimon in #8
• Add coverage and docs in CI by @gromdimon in #19
• feat: Migrate to Typer for CLI by @gromdimon in #22
• Configure setuptools packaging by @gromdimon in #25
• Restructure seqvar pvs1 computation logic by @gromdimon in #27
• rename types to defs by @gromdimon in #28
• Increase code coverage by @gromdimon in #29
• Add mehari tests by @gromdimon in #32
• Add support of Structural variants by @gromdimon in #36
• Add strucvar pvs1 decision tree by @gromdimon in #38
• Improve documenttion by enhancing docstrings by @gromdimon in #40
• Add example variants list used for development and tesing by @gromdimon in #33
• Description of prediction path by @gromdimon in #58
• Add lfs tracking for json files by @gromdimon in #62
• Replace autopvs1 with auto-acmg by @gromdimon in #65
• Alternative start codon rule by @gromdimon in #67
• Restructure module in order to support other acmg rules by @gromdimon in #83
• Remove duplicated .env in gitignore by @gromdimon in #82
• Add documentation of acmg criteria by @gromdimon in #85
• Add bibliography note by @gromdimon in #87
• Implement new annonars model by @gromdimon in #88
• Add more tests for functionality with annonars by @gromdimon in #91
• Integrate loguru for advanced logging by @gromdimon in #93
• Setup proper error handling throughout the application by @gromdimon in #94
• Implementation of PS1 criteria by @gromdimon in #95
• New variants and new links for various sources by @gromdimon in #96
• End2end tests by @gromdimon in #97
• Increase test coverage by @gromdimon in #100
• Fix NMD prediction by @gromdimon in #101
• Implement _upstream_pathogenic_variant method by @gromdimon in #102
• Refactoring by @gromdimon in #105
• Add loguru to requirements.txt in docs by @gromdimon in #107
• Implement BA1, BS1, BS2, PS4, PM2 criteria by @gromdimon in #106
• Unify auto-acmg methods by @gromdimon in #110
• Implement pm1 criteria by @gromdimon in #111
• Implement PP2 and BP1 criteria by @gromdimon in #112
• Implement bp7 criteria by @gromdimon in #113
• Added depricatioin note for PP5 and BP6 criteria by @gromdimon in #114
• Init pp3 and bp4 implementation by @gromdimon in #115
• New result class by @gromdimon in #116
• Implement exon skipping or cryptic ss disruption method by @gromdimon in #124
• Implement SpliceAI scores check and proximity to the splice site check for the AutoBP7 by @gromdimon in #125
• Finish autopp3bp4 by @gromdimon in #126
• Enhance general output of acmg prediction by @gromdimon in #128
• Finish AutoPP2BP1 by @gromdimon in #129
• Reimplement AutoPS1PM5 by @gromdimon in #130
• Finish prediction of BA1, BS1, BS2, PM2 criteria by @gromdimon in #131
• Finish Autopm4bp3 by @gromdimon in #132
• Finish AutoPM1 by @gromdimon in #133
• Minor LFS PR by @gromdimon in #135
• Renme some methods by @gromdimon in #137
• Add Comparison scripts by @gromdimon in #138
• Comparison of VarSome by @gromdimon in #139
• Genebee results by @gromdimon in #140
• Results comparison v2 by @gromdimon in #141
• Renaming: positive to met, negative to unmet by @gromdimon in #142
• Rename AutoBA1BS1BS2PM2 to AutoPM2BA1bS1BS2 by @gromdimon in #143
• Example output file by @gromdimon in #144
• Remove unnecessary notebooks by @gromdimon in #145
• Implement caching for API by @gromdimon in #147
• Add paginated annonarse range queries by @gromdimon in #149
• Adapt pydantic models by @gromdimon in #150
• New results by @gromdimon in #152
• BA1 updates by @gromdimon in #153
• Fix failing tests by @gromdimon in #154
• Additional information for kappa values by @gromdimon in #155

New Contributors

• @gromdimon made their first contribution in #12

Full Changelog: https://github.com/bihealth/auto-acmg/commits/v0.1.0