'make test && ./test'
runs the unit tests

'make benchmark && ./benchmark input.txt [times]'
runs an benchmark using the provided input text. If times is given, an
average over 'times' runs is reported.

'make dalign &&
./dalign diploid1.txt diploid2.txt map1.txt map2.txt haploid.txt ref_len'
computes the edit distance between the haploid and the best
recombination of the diploids. The genome input files are expected to
contain only the actual genome string in ASCII. The map files are to
contain one index per line. The last parameter, ref_len, is the length
of the original reference to which the map files refer to.
