update readme #6
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- Added typing_extensions (used in cli.py for type annotations) - Added requests (used in cli.py for downloading reference genomes) - Added scikit-learn to requirements_dev.txt (already in setup.py) - Cleaned up formatting in requirements_dev.txt
CLI improvements: - Add support for compressed VCF files (.vcf.gz) - Derive output CSV filename from input sample name - Filter out empty rows with zero mutations from genotyped VCFs - Improve signature filtering with better error messages Example data updates: - Add COSMICv34_cns.txt signature reference file - Add tcga_coad_single.vcf.gz example VCF file - Remove small_genome.fa (replaced with better examples)
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Nov 25, 2025
Merge pull request uio-bmi#6 from cdbope/master
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