$ 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)
$