Add diagnostic logging to --RefVCF SVD generation pipeline#79
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The --RefVCF code path had minimal progress or diagnostic output, making it difficult to troubleshoot issues like unexpected marker filtering or slow SVD computation. Add logging: - Per-chromosome marker counts after VCF reading, so users can verify the right chromosomes are included and see marker distribution - Progress notices for genotype matrix construction and SVD computation - Summary of output files written by WriteSVD - Improve existing marker/individual count messages
Griffan
previously approved these changes
Apr 11, 2026
Griffan
approved these changes
Apr 11, 2026
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The --RefVCF code path had minimal progress or diagnostic output, making it difficult to troubleshoot issues like unexpected marker filtering or slow SVD computation.
Add logging: