Running notes on non-obvious design decisions and gotchas, so future work (and future sessions) don't re-derive them. One topic per file.
- scaffold-enumeration.md — why V×J only (not V×D×J), dedup, N-spacer.
- reading-frames.md — V frame detection, J frame from aux, FR4 sanity check.
- igblast-gotchas.md — dummy D db, IGDATA, aux files, AIRR coords.
- markup-transfer.md — runtime projection, indel/strand semantics, D-segment TODO.
- mmseqs-params.md — tuned nt/aa params, all-loci single DB, caching, speedup.
- discordance-and-scaling.md — why arda≈IgBLAST, alignment-phase frame fix, bulk RNA-seq prefilter speed, 30M-read estimate.
- cluster-slurm.md — split/merge/slurm sharding design + how it's tested without a cluster.