clinvar-this 0.4.0

ClinVar Submission via API Made Easy

ClinVar This!

ClinVar Submission via API Made Easy

• Free software: MIT license
• Documentation: https://clinvar-this.readthedocs.io/en/latest/
• Discussion Forum: https://github.com/bihealth/clinvar-this/discussions
• Bug Reports: https://github.com/bihealth/clinvar-this/issues

Getting Started

Documentation

You can find comprehensive documentation here:

• https://clinvar-this.readthedocs.io/en/latest/

A good place to start is:

• "Getting Started" in the documentation

Changelog

0.4.0 (2023-09-06)

Features

• add command to extract gene-to-phenotype links (#104) (#106) (b3b323a)
• adding --version option (#110) (7f3b091)
• adding command to generate per-gene impact report (#102) (#103) (c86a5c7)
• adding missing clinvar measure set (#109) (f0f64e0)
• adding support for parsing ClinVar XML (#99) (#100) (c673f7d)
• command to extract variants per ACMG class and freq. (#107) (#108) (c623f6d)

Bug Fixes

• making conversion more robust, indicate errors (#105) (8333aea)

0.3.0 (2023-09-04)

Features

• removing versioneer in favour of version from release-please (#95) (5b922bb)

Bug Fixes

• using varfish-bot token for release-please (#97) (35fad52)

0.2.1 (2023-03-17)

Bug Fixes

• fixing strucvar export (#84) (1050a67)
• sequence variant export (#82) (0fe3fb9)

0.2.0 (2023-03-15)

Features

• add support for SV TSV files (#75) (#78) (d4fffce)

Documentation

• add badges to readme (#65) (207038c)
• adding file format documentation (#71) (3a04ffd)
• extending docs; getting started from README (#44) (#68) (77892f0)
• updating docs introduction section (#67) (d6c865b)

0.1.0 (2022-12-02)

Features

• add basic config management in CLI (#32) (#33) (c903546)
• add functions for managing batch data (#34, #37) (#35) (0c7e0f9)
• add sphinx-based documentation (#30) (#31) (d10adc5)
• add tests for submission messages (#19) (#22) (b168d47)
• add unit tests for submission messages (#19) (#20) (1c4e11a)
• adding mypy type checking (#11) (#12) (700994a)
• adjust to ClinVar API change (Nov 2022) (#47) (#48) (0e4fb50)
• allow annotation with HPO terms in TSV format (#50) (#56) (0b0da41)
• allow import of extra columns (#53) (#54) (616bfe7)
• completing enums (#23) (#24) (9198983)
• implement api models (#4) (#5) (3690c36)
• implement attrs-based message models (#1) (#2) (f253c24)
• implement enums for submission messages (#14) (#16) (201cbe4)
• implement internal models for submissions (#9) (#26) (be04e40)
• implement minimal TSV format (#17) (#18) (960827d)
• implement models for extra files (#6) (#13) (852e4c6)
• implement models for submission message (#8) (#15) (90afd10)
• implement more columns in TSV (#39) (#55) (6184d76)
• implementing REST clinvar_api.client module (#28) (#29) (829d907)
• store errors from "batch retrieve" (#59) (#60) (67b8b0c)
• write data into profile sub directory (#52) (e699736)

Bug Fixes

• interpret TSV OMIM "not provided" (#57) (#58) (b655097)

Documentation

• add getting started tutorial to README (#45) (#61) (3de084b)