genmod - Stable sorts to help container testing

[3.10.1]

Fixed

• Documentation formatting for more modern mkdocs (pages to nav) (#168)
• Stable sort in bioconda (BusyBox sort) not recognizing long options (#170)
• Unstable Annotation= order in genmod annotate --regions (#173)

- Python
Published by dnil 11 months ago

genmod - Bugfixes to sorting, chrM and empty files. Allow modern python, and uv with hatchling build system.

[3.10]

Changed

• Use uv with hatchling to build and publish (#104)
• Automation for Docker publish and mkdocs githubio (#161) ### Fixed
• The optional fields Source and Version are allowed in the VCF header(#106)
• Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) (#142)
• Update annotation examples (#144)
• Updated documentation with warning about compounds only being scored within the first family in the VCF (#151)
• Fixed sorting of variants (#152)
• genmod annotate for mitochondrial variants when using the chrM notation (#157)
• Fix linting issues (#154)
• genmod models adds headers to VCF even if it contains no variants (#160)

- Python
Published by dnil 12 months ago

genmod - 3.9

What's Changed

• Ensure chrX and X are treated equally by @fellen31 in https://github.com/Clinical-Genomics/genmod/pull/135
• Add GitHub Actions workflows for PyPI and CHANGELOG by @fellen31 in https://github.com/Clinical-Genomics/genmod/pull/136
• Add parameters for penalty and threshold by @Jakob37 in https://github.com/Clinical-Genomics/genmod/pull/138
• Update readme by @dnil in https://github.com/Clinical-Genomics/genmod/pull/140
• Bump version to 3.9 by @dnil in https://github.com/Clinical-Genomics/genmod/pull/139

New Contributors

• @Jakob37 made their first contribution in https://github.com/Clinical-Genomics/genmod/pull/138
• @dnil made their first contribution in https://github.com/Clinical-Genomics/genmod/pull/140

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.8.3...3.9

- Python
Published by dnil over 1 year ago

genmod - 3.8.3

What's Changed

• Fix unstable variants in models output by @fellen31 in https://github.com/Clinical-Genomics/genmod/pull/134

New Contributors

• @fellen31 made their first contribution in https://github.com/Clinical-Genomics/genmod/pull/134

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.8.2...3.8.3

- Python
Published by fellen31 over 1 year ago

genmod - 3.8.2

What's Changed

• setup.py: Lockdown genmod, limit compatibility to python v3.8 by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/120
• Export Rankscore as Float Type by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/122
• setup.py: Set version 3.8.2 by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/123

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.8.1...3.8.2

- Python
Published by torbjorgen about 2 years ago

genmod - 3.8.1

What's Changed

• setup py uplift requirements by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/117
• setup.py: Set version 3.8.1 by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/118

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.8.0...3.8.1

- Python
Published by torbjorgen over 2 years ago

genmod - 3.8.0

What's Changed

• Rankscore normalization by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/108
• CHANGELOG, setup.py changes for v3.8.0 by @torbjorgen in https://github.com/Clinical-Genomics/genmod/pull/114

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.7.4...3.8.0

- Python
Published by torbjorgen over 2 years ago

genmod - 3.7.4

What's Changed

• set abstractsocketssupported to False by @ramprasadn in https://github.com/Clinical-Genomics/genmod/pull/111

New Contributors

• @ramprasadn made their first contribution in https://github.com/Clinical-Genomics/genmod/pull/111

Full Changelog: https://github.com/Clinical-Genomics/genmod/compare/3.7.3...3.7.4

- Python
Published by ramprasadn over 2 years ago

genmod - Updates click dependency

Use click < 7.0

- Python
Published by moonso over 7 years ago

genmod - Version 2.0

• More modular for easier maintenance
• Improvements to scorer

- Python
Published by moonso about 11 years ago

genmod - Split Multialleleic Calls

• genmod can now split multi alleleic calls. Use -split/--split_variants flag.
• use -p/--processes to manually decide the number of processes to be used for annotation

- Python
Published by moonso about 11 years ago

genmod - Annotates multiple families

The annotattion is now based on which family that follows an inheritance pattern, not only which variant. Annotation now looks like: - GeneticModels=fam_id_1:AR_hom,fam_id_2:AR_hom|AR_hom_dn - Compounds=fam_id_1:1_2456_A_C,fam_id_2:1_24563_A_C|1_23564_C_T

- Python
Published by moonso about 11 years ago

genmod - v1.7

• Changed pysam -> pytabix
• Changed annotation of 1000GMAF -> 1000G_freq
• Added support for annotating with ExAC frequencies
• Added summarize_variants

- Python
Published by moonso over 11 years ago

genmod - genmod analyze

• Changed structure of some files for better overwiew
• Fixed an issue with compounds when both parents have the mutation
• Added genmod analyze (se documentation)

- Python
Published by moonso over 11 years ago

genmod - Add doi

Added a doi tag

- Python
Published by moonso over 11 years ago