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CFSAN-Biostatistics / phraya Public

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feat: implement phraya filter CLI (closes #85)#112

Merged

crashfrog merged 11 commits into

mainCFSAN-Biostatistics/phraya:mainfrom

worktree-agent-a2d99b6ab67d489dfCFSAN-Biostatistics/phraya:worktree-agent-a2d99b6ab67d489dfCopy head branch name to clipboard

Jun 1, 2026

Conversation Commits11 (11)Checks Files changed

Merged

feat: implement phraya filter CLI (closes #85)#112
crashfrog merged 11 commits into
mainfrom
worktree-agent-a2d99b6ab67d489df

Commits

Commits on Jun 1, 2026

test: add acceptance tests for #85 (phraya filter CLI)

crashfrog
and
claude
committed
feat: implement filter subcommand with VCF/TSV/phraya output
crashfrog
committed
fix: calculate coverage as sum of allele counts for filtering
crashfrog
committed
debug: add temporary debug output for filter testing
crashfrog
committed
debug: add command type debug output
crashfrog
committed
debug: detailed observation logging
crashfrog
committed
debug: print raw observations
crashfrog
committed
cleanup: remove debug statements
crashfrog
committed
debug: include filter params in statistics message
crashfrog
committed
revert: use local_coverage for coverage filtering
crashfrog
committed
cleanup: remove debug filter params from statistics message
crashfrog
committed

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