Releases | Open Source Science

https://github.com/clinical-genomics/fusion-report - Release v4.0.1

update README

- Python
Published by clingen-sthlm 8 months ago

https://github.com/clinical-genomics/fusion-report - Release v4.0.0

Added

Added support to run the tool without SSL chain verification for users behind proxy servers who act as MITM https://github.com/Clinical-Genomics/fusion-report/pull/79
Added support for [CTAT-LR-Fusion](https://github.com/TrinityCTAT/CTAT-LR-fusion), which supports the fusion calling in PacBio or Nanopore long reads data https://github.com/Clinical-Genomics/fusion-report/pull/82,https://github.com/Clinical-Genomics/fusion-report/pull/83 .

Changed

Updated COSMIC database to be compatible with the new SANGER websitehttps://github.com/Clinical-Genomics/fusion-report/pull/83

Updated project to be compatible with Python 3.12 https://github.com/Clinical-Genomics/fusion-report/pull/83

Updated GitHub Actions workflow to use latest actions versions https://github.com/Clinical-Genomics/fusion-report/pull/83

The score is now called Fusion Indication Index (FII) https://github.com/Clinical-Genomics/fusion-report/pull/83

FII formula changed https://github.com/Clinical-Genomics/fusion-report/pull/83: $$ FII = 0.5 * \sum_{tool}^{tools provided} f(fusion, tool) + 0.5 * \sum_{db}^{dbs provided} g(fusion, db)*w(db) $$

Weights for databases are as follows:
    COSMIC (50)
    MITELMAN (50)
    FusionGDB2 (0)

- Python
Published by clingen-sthlm 11 months ago

https://github.com/clinical-genomics/fusion-report - Release v3.1.4

Fix bumping | major (#84)

formatting
ruff fixes
fix syntax

- Python
Published by clingen-sthlm 11 months ago

https://github.com/clinical-genomics/fusion-report - Release v3.1.3

update cosmic and use FII 50%DBs 50%tools | MAJOR (#83)

update cosmic and use FII 50%DBs 50%tools
adapt to 3.12
update black and reformat
cleanup bump version
update setup
re-add init
update setup
add starfusionlr to toolsprovided
add starfusion_lr into tools provided
add pr link
rename starfusionlr to ctatlr_fusion
update documentation about the formula
remove log file

- Python
Published by clingen-sthlm 11 months ago

https://github.com/clinical-genomics/fusion-report - Release 3.1.2

Add the support for the tool: CTAT-LR-Fusion (#82)

add the support for ctat-lr-fusion
lower the name
add test for starfusion_lr
add ctat-lr-fusion to supported tools
add changelog for support of CTAT-LR-Fusion
reformat by black

Co-authored-by: Haidong Yi haidong.yi@stjude.org Co-authored-by: haidyi haidongyi@gmail.com

- Python
Published by clingen-sthlm 11 months ago

https://github.com/clinical-genomics/fusion-report - Release 3.1.1

Bump version to 3.1.0 (#80)

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/fusion-report - 3.1.0

What's Changed

[3.1.0] Added

Added support to run the tool without SSL chain verification for users behind proxy servers who act as MITM
Add no_ssl parameter as flag to verify or not by @rannick in https://github.com/Clinical-Genomics/fusion-report/pull/79

Changed

Scoring formula changed to: $$ score = 0.8 * \sum_{tool}^{tools provided} f(fusion, tool) + 0.2 * \sum_{db}^{dbs provided} g(fusion, db)*w(db) $$

Weights for databases are as follows:
    COSMIC (50)
    MITELMAN (50)
    FusionGDB2 (0)

[3.0.0] Added

Options --no-cosmic/--no-fusiongdb2/--no-mitelman to download and run without those specified databases

- Python
Published by rannick over 1 year ago