$ make -C src all $ ./src/main Usage: ./src/main [OPTION]... Indexes and queries a set of STs. The input must be a tab separated vector of integers, with the same length per line. Options: -i INAME The name for the index (mandatory). -q K List matches with at most K errors. -b The index should be (re)built. $ xzcat campylobacter.unique.csv.xz | ./src/main -i campylobacter -b [0.001227] Loading data... 5446 alleles 5669 profiles [2.073521] Constructing SA and ISA... [14.476156] Writing index... [14.702880] done! $ ls campylobacter.??? campylobacter.ids campylobacter.idx $ xzcat campylobacter.unique.csv.xz | tail -n 1 > query $ ./src/main -i campylobacter -q 30 < query 5668 0 #hits: 1 (962) $