v1.4.0 — comparesketch --low-mem streaming mode
Features
comparesketch --low-mem: streaming M×N comparison for large reference sets.
The default mode pre-caches every reference's k-mer hashes (M+N file reads), but its
memory scales with the entire reference universe — for a few thousand multi-megabase
genomes this can exceed 1 TB. With--low-mem, only one Bloom filter and one
reference's k-mers are held per thread at a time: each first-set reference is loaded
into a filter, and every second-set reference is re-read from disk and queried against
it. Memory becomes O(threads × genome) instead of O(all genomes), at the cost of
M×N (rather than M+N) file reads. The similarity output is identical to the default
mode; only the memory/I/O profile changes.
Full changelog: https://github.com/amazon-science/uniqsketch/blob/main/CHANGELOG.md