Dev-GCGI-1446_fusion-total #498
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added 4 commits
December 4, 2024 11:25
…fter filtering by OncoKB levels
AqsaAlam
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Dec 4, 2024
iainrb
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OumaimaHamza
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Dec 16, 2024
* Dev gcgi 1378 new gsicapbench inputs (#486) * Update default sample names and placeholder IDs/purity * Simplify by removing the benchmark_params.json file * Add new JSON diff script and tests * Added patient study id raw * Updated changelog * Allowed tumour and normal ids to be manually specified for provenance helper * Added oncokb definitions to 40x assays * Dev-GCGI-1446_fusion-total (#498) * Debugging * Debugging * Update clinically relevant variants count to reflect unique fusions after filtering by OncoKB levels * Update test checksum --------- Co-authored-by: Oumaima Hamza <[email protected]> * self.patient_id_raw defaults to None when not in use -- instead of being undefined, which causes an error * Dev gcgi 1326 whizbam links for fusions (#487) * Dump to json output * Process fusions and generate blob URLs from json template * gzip instead of pysam * skip header to use index * debugging * Fix column names * debugging * Fix genes combination scenario * Get template json * Specify path to file under plugin dir * no message * template json path * debugging * Reformat breakpoint * Search for bam and bai files * Use Node.js script for compression * Get tumour ID * Add positional argument * Add compression script relative path * Fix path * Change to CommonJS syntax * Add js scripts for compression * Convert to to CommonJS syntax * convert to CommonJS syntax * Compression using pysam.bgzip * base64 encoding * Convert into URL safe base64 * Mimic the JavaScript behavior * Fix blob URL format * Fix base64 encode * Compress json not the path to the file * Change whizbam URL * Change csv to tsv file * Fix and refactor fusion test * Changelog * Respond to PR comments: Improve warning/error messages and replace hardcoded values with variables * Clean up process_fusion function by adding helper functions * Add custom error class * Add whizbam_project parameter to the fusion plugin * Optimizing checks for files existence and URL assignment * Fix warning logging --------- Co-authored-by: Oumaima Hamza <[email protected]> * Release 1.7.8 update (#500) * Update changelog and version.py * Revert "Update changelog and version.py" This reverts commit 97bf3d7. * Update changelog and djerba version * Revert "Update changelog and djerba version" This reverts commit 26e27ac. * Update changelog and djerba version --------- Co-authored-by: Oumaima Hamza <[email protected]> * Refactor fusion plugin test; move setup operations to setUp(self) * Remove self.maxDiff = None --------- Co-authored-by: Iain Bancarz PhD <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Oumaima Hamza <[email protected]>
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