Add functionality to parse variants from VCF files #6
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* Initial commit * Update DESCRIPTION * bootstrap tests * Test CI * Prototype function to load gene expression data to SE * Stub functions * Add progress bar * Add pre-commit config * Add personalis functions to package and run roxygen * Add relevant documentation on personalis outputs * Update exploratory notebook * Fix pre-commit prettier * Format files according to pre-commit checks * Draft function to read small variant data * configure lintr * Implement basic functionality to read variant and GEX data into MAE * Implement basic error handling for missing samples * Generalize warning for missing samplese * Read CNV data * Fix CNV IO function in case of empty tables * Add function to read personalis HLA data * Add function to read in TCR data * Scrape TCR summary statistics from HTML * Implement function to read somatic variant statistics * Read summary stats for somatic variants * Implement bumpy_matrix_to_df * Read CNV summary statistics * Read MSI info * refactor * Workaround for samples with no col in bumpy matrix * Apply the fix also to small variant data * Use "Genomic Variant" instead of pos as unique variant identifier * Fix issue with reading non-somatic variants * Handle case when there are no samples for a modality * Fix duplicated mutation ids * Fix column name incompatibility in newer HTML report versions * stub vignette * Add vignette * Update vignette * Ensure bumpy matrix, row and coldata have consistent order * Fix alternative gex filename and CNV import * Support alternative TCR path * Fix column conversion in CNV reader * Fix paths * add function for parsing VCF files * add functionality for reading and storing VCF data * add/change comments * add option to read small variant reports of type all * Angewendeter Vorschlag * Angewendeter Vorschlag * add sample type check * Angewendeter Vorschlag * Angewendeter Vorschlag * add report_type parameter * Update README * Fix reading CNV report * Roxygenize * Fix parse copy number report --------- Co-authored-by: Christopher Mohr <[email protected]> Co-authored-by: grst <[email protected]>
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Porting changes originally made by @christopher-mohr.