Indexing

[ksahlin]

Note to developer:

1. Separate indexing from alignment so that we can throw out 64-bit hash from flat vector when hash table is built - reduces memory during alignment a bit.
2. Indexing speed: Parallelize seed extraction over chromosomes. (3. About 50% of the time is sorting the flat vector and building hash table though, faster sorting could be performed with radix sort as in minimap2.)