Rewrite processSequenceVariations#4

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jbrestel wants to merge 42 commits intomainfrom

merge-experiments-refactor

Commits on Jan 24, 2026

Commits on Jan 25, 2026

Replace VarScan with FreeBayes for variant calling

jbrestel
and
claude
committed

Commits on Feb 1, 2026

Rewrite processSequenceVariations in Julia

jbrestel
and
claude
committed

Commits on Feb 6, 2026

ProcessSingleExperiment functional. Using unmasked reference sequence for bcftools consensus, and then masking later.
rdemko2332
committed

Commits on Feb 10, 2026

Commits on Feb 13, 2026

wip
jbrestel
committed

Commits on Feb 20, 2026

Commits on Feb 27, 2026

Commits on Mar 4, 2026

update claude.md
jbrestel
committed

Commits on Mar 6, 2026

Commits on Mar 10, 2026

Commits on Mar 12, 2026