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Recent Releases of https://github.com/clinical-genomics/stranger

https://github.com/clinical-genomics/stranger - TRGT MotifCount, PathologicStruc and TRID parsing fixes

[0.9.5]

Added

  • More tests for trgt repeats parsing ### Changed
  • Updated build actions, set Docker build provenance, use two-stage build and a non-root user for Docker image ### Fixed
  • Set STR_STATUS to most severe consequence for given repeat strings (TRGT decompose)
  • More TRGT PathologicStruc locus annotations to demo resources
  • Always check and export TRGT repeat keys as well
  • Motif counts for TRGT alleles erroneously summed
  • TRID for a couple of STRchive style entries with "_" need exact matching since the gene id alone is not unique

- Python
Published by dnil 12 months ago

https://github.com/clinical-genomics/stranger - Fix bug with no ref on multi-allele TRGT FORMAT decompose

[0.9.4]

Fixed

  • Bug with no ref on multi-allele FORMAT decompose

What's Changed

  • Decompose missing ref by @dnil in https://github.com/Clinical-Genomics/stranger/pull/85
  • bump to v0.9.4 by @dnil in https://github.com/Clinical-Genomics/stranger/pull/87

Full Changelog: https://github.com/Clinical-Genomics/stranger/compare/v0.9.3...v0.9.4

- Python
Published by dnil about 1 year ago

https://github.com/clinical-genomics/stranger - `setuptools` import issue and switch build system to `uv`

[0.9.3]

Fixed

  • Switch build system to uv-hatchling
  • Version from importlib metadata

- Python
Published by dnil over 1 year ago

https://github.com/clinical-genomics/stranger - Fix output of multi individual format and unannotated loci

[0.9.2]

Fixed

  • Use codecov badge and fix scout link on README page
  • Added a test for TRGT MCs set to .
  • Added CLI test for TRGT file
  • Codecov upload hidden artifact issue
  • Incorrect multisample, multiallele FORMAT output
  • Write unannotated entries (not in definition file) to output (reverted to pre-0.9 behaviour)

- Python
Published by dnil over 1 year ago

https://github.com/clinical-genomics/stranger - v0.9.1

[0.9.1]

Added

  • Added github action test and release workflows ### Fixed
  • Docs for TRGT annotation
  • Fallback setting allele size to 0 if MC is only set to "." and TRGT annotation requested

- Python
Published by dnil almost 2 years ago

https://github.com/clinical-genomics/stranger - Support for TRGT VCFs

[0.9.0]

  • Add Docker image
  • Parse TRGT VCFs - in particular, decompose and parse FORMAT.MC
  • Bring in updated loci references from raredisese reference-files
  • Fix processing TRGT VCFs with missing MC and TRIDs without underscore [#59(https://github.com/Clinical-Genomics/stranger/pull/59)
  • Updates to pathogenic motifs for two loci: RFC1, RAPGEF2

- Python
Published by dnil about 2 years ago

https://github.com/clinical-genomics/stranger - Catalog patch DAB1, POLG

  • Fix DAB1 pathologic repeat unit name Update POLG coords, quite a bit on hg38

- Python
Published by dnil over 4 years ago

https://github.com/clinical-genomics/stranger - Ob1 corrections, with a little help from my friends

[0.8.0]

Off by one error on PathogenticMin output. All affected have at least been cautioned premutation with proper size. Added script to check HGNCId-symbol correspondence against genenames.org. Added script to compare two variantcatalogs and warn on disagreeing field items. Sync min/max between hg19, hg38 for ATN1, DMPK, FMR1 and TBP.Update BEAN1 documentation reference. Update PABPN1 source tag. Update GLS and RFC1 hg19 coordinates (zero based off by one). Update NIPA1 locus definition updating hg19 to the current ExHu one. Update ARX and SOX3 0-based off by one. Usually unproblematic, but gives ugly gap on REViewer alignments. Update HTT PathogenicMin and NormalMax so already reduced penetrance are pathogenic - and mark intermediate pre_mutation. Update pathologic region annotation on (mostly hg38 liftOver) loci affecting alternate region naming for ATXN7, ATXN8OS, FXN, HTT, CNBP, NOP56. Update DAB1 repeat unit (revcomp) and off by one coordinates.

- Python
Published by dnil almost 5 years ago

https://github.com/clinical-genomics/stranger -

Increase rank score to get above CG default loading threshold.

- Python
Published by dnil over 5 years ago

https://github.com/clinical-genomics/stranger - Add a family_id option and print to RankScore elements

  • Add a family_id option and print to RankScore elements

- Python
Published by dnil over 5 years ago

https://github.com/clinical-genomics/stranger - Get a DOI

This release is created to autogenerate a DOI

- Python
Published by moonso about 6 years ago

https://github.com/clinical-genomics/stranger - The one with limits

Add normal and pathologic limits for each variant to the VCF.

- Python
Published by dnil over 6 years ago

https://github.com/clinical-genomics/stranger - The one with the default json file included

[0.5.4]

Update Manifest to include json resource file.

- Python
Published by dnil about 7 years ago

https://github.com/clinical-genomics/stranger - Dual REPID types.

[0.5.3] Allow both REPID naming systems. Make json file default, and include as a resource in the PyPi distribution. Update normal range for AFF2 and TBP.

- Python
Published by dnil about 7 years ago

https://github.com/clinical-genomics/stranger - ExHu v3.0 REPID naming

Updated REPID naming to match release version of ExHu 3.0. Also compatible with older ExHu, but not the v3rc series.

- Python
Published by dnil about 7 years ago

https://github.com/clinical-genomics/stranger - The one with OPMD

[0.5.1]

Added PyPi badge to README.md. Added disease name for OPMD.

- Python
Published by dnil about 7 years ago

https://github.com/clinical-genomics/stranger - The one for ExpansionHunter 3.0.0-rc1

Adapts to new ExpansionHunter format. If you still use pre-3 versions of ExpansionHunter, please stay at v0.4 of Stranger.

- Python
Published by dnil over 7 years ago