Devel pre v4#576

Merged

jonathangoeke merged 23 commits intodevel_pre_v4_jgfrom

Apr 23, 2026

Commits on Apr 15, 2026

refactor(args): rename demultiplexed to extractBarcodeUMI, remove cleanReads/sampleNames/barcodesToFilter, drop CSV input for demultiplexed and clusters
ch99l
committed
fix: adjust NDR threshold behavior. Previously, NDR = 1 would override `remove.subset` and `min.sampleNumber`. Now, NDR = 0.999 and NDR = 1 produce identical results except for the NDR threshold it…
SuiYue-2308
committed
feat: add bambu.singlecell and bambu.spatial wrapper functions
ch99l
committed
Move min.exonDistance, min.primarySecondaryDist, min.primarySecondaryDistStartEnd1/2 from opt.discovery into a new opt.rcAssignment parameter with its own setRcAssignmentParameters().
SuiYue-2308
committed

Commits on Apr 17, 2026

Commits on Apr 20, 2026