vdjtools 5.3.1

Exact cohort distances now aggregate each sample once and use existing sparse matrix products for cohorts of four or more samples. Direct comparisons remain in place for three or fewer samples, and Pearson/fuzzy overlap paths keep their existing arithmetic and engines.

• Floor logarithmic overlap distances at zero so identical repertoires can be hierarchically clustered.
• Stream corpus SHA256 checks in bounded memory and close NPZ archives on both success and read/validation failures.
• Validate preinitialized Polars pools against the current CPU allocation before sample maps, including the single-worker path; process workers retain serial inner kernels.
• Explain exact-overlap formulas, memory requirements, CPU budgets, and the scope of OLGA concordance and performance measurements.

Measured on 64 synthetic samples with 1,000 clonotypes each, the four exact-distance metrics improve 17.6–19.7x over pairwise assembly. Three samples with 10 million clonotypes retain the previous direct path and exact results. These workload measurements do not imply universal core-linear scaling.

Native algorithms, model parameters, and dependency floors are unchanged from 5.3.0. The license and badge remain aligned with ARDA.