https://github.com/cfia-ncfad/wgscovplot - 1.0.2 - Clair3 VCF parsing fix

This patch release fixes an issue with not capturing an EmptyDataError when reading VCF files and an issue where Clair3 VCFs from non nf-flu analyses are prematurely converted to a dict from a Pandas DataFrame.

Other Changes

• dev: Update type hints given mypy and ruff linting
• fix: check BAM files for reference sequence ID/name in addition to Mosdepth files. Improved searching for the reference sequence GFF and FASTA in the input directory before trying to fetch from NCBI.

What's Changed

• fix: Clair3 VCF parsing by @peterk87 in https://github.com/CFIA-NCFAD/wgscovplot/pull/57

Full Changelog: https://github.com/CFIA-NCFAD/wgscovplot/compare/1.0.1...1.0.2

- JavaScript
Published by peterk87 about 2 years ago

https://github.com/cfia-ncfad/wgscovplot - 1.0.1 - Pydantic patch

This patch release fixes #55 and sets the minimum required version of Pydantic to V2.

What's Changed

• Set min version of Pydantic to 2.0.0 by @peterk87 in https://github.com/CFIA-NCFAD/wgscovplot/pull/56

Full Changelog: https://github.com/CFIA-NCFAD/wgscovplot/compare/1.0.0...1.0.1

- JavaScript
Published by peterk87 over 2 years ago

https://github.com/cfia-ncfad/wgscovplot - 1.0.0

This is a major release of wgscovplot with many user experience and quality of life changes to make the tool easier to run and use. The frontend (HTML output) has been almost completely rewritten to have more of a single-page app (SPA) like feel.

There are also a number of improvements to the developer experience so that frontend dev can be done separately with live-code reloading using real-world datasets.

• Calculate depths from BAM files if Mosdepth per-base.bed.gz not found.
• SolidJS instead of JQuery for UI
• Migrated to Typescript and TSX from JS for frontend code.
• Hatch for packaging, building and managing project. Migrated from setup.py to pyproject.toml.
• Removed compiled JS from repo. JS/TS is compiled at build time with npm or bun if installed (hatch_build.py).
• Migrated from Webpack to Vite for frontend dev and JS compilation.
• Migrated from Bootstrap CSS to Tailwind CSS
• Added frontend test datasets and profiles for isolated frontend dev. See web/README.md for details.
• Moved CLI test data for easier testing with segmented and non-segmented virus pipeline output
• Added Black formatting, Ruff linting and Mypy type checking.
• Fixed variant bar colours to represent ALT allele rather than REF.
• Simplified CLI options with auto-detection of files and parameters based on type of analysis results provided.
• Coverage depths are compressed by default to base64 encoded string in HTML output to reduce HTML output size.
• Added more coverage plot visual customization options for colours, fonts, sizes, etc.
• Removed Jest JS/TS testing for now.

What's Changed

• WIP: Major refactor by @peterk87 in https://github.com/CFIA-NCFAD/wgscovplot/pull/45
• SolidJS, Hatchling update by @peterk87 in https://github.com/CFIA-NCFAD/wgscovplot/pull/50
• Release 1.0.0 by @peterk87 in https://github.com/CFIA-NCFAD/wgscovplot/pull/52

Full Changelog: https://github.com/CFIA-NCFAD/wgscovplot/compare/v.0.3.0...1.0.0

- JavaScript
Published by peterk87 over 2 years ago

https://github.com/cfia-ncfad/wgscovplot - wgscovplot v0.3.0

0.3.0 (2022-08-31)

:warning: Major changes

• Add support for segment virus (AIV)
• Accept result folder generated by nf-flu with option --segment-virus
• Annotate primer sequences with option --primer-seq. The primer sequence in fasta file

- JavaScript
Published by nhhaidee almost 4 years ago

https://github.com/cfia-ncfad/wgscovplot - wgscovplot v0.2.1

0.2.1 (2022-06-14)

:warning: Minor fixes

Fixed issues of tooltips displayed incorrectly due to samples list being reversed

- JavaScript
Published by nhhaidee about 4 years ago

https://github.com/cfia-ncfad/wgscovplot - wgscovplot v0.2.0

0.2.0 (2022-03-29)

:warning: Major changes

• Automatically Gene Bank and reference retrieval
• Automatically detect amplicon data and option to toggle amplicon bar
• Variant heat map is updated according to selected samples
• Downgrade and use Echarts v5.2.2 to fix the problem of amplicon plot (https://github.com/nhhaidee/wgscovplot/issues/36)
• Clean up code.

- JavaScript
Published by nhhaidee over 4 years ago

https://github.com/cfia-ncfad/wgscovplot - wgscovplot v0.1.1

0.1.1 (2022-03-18)

:warning: Minor fixes

Fixes parsing of Medaka VCF with low/no coverage variants.

- JavaScript
Published by nhhaidee over 4 years ago

https://github.com/cfia-ncfad/wgscovplot - wgscovplot v0.1.0

[0.1.0] - 2022-03-04

The first release of wgscovplot

- JavaScript
Published by nhhaidee over 4 years ago