Alignment of long reads

[ksahlin]

Note to developer:

1. Use Randstobes order n=3.
2. Collinear chaining: is needed, perhaps heuristic by sorting based on reference (see find_NAMs_alt() function)
3. How to implement split mapping?
4. Need partitioned local alignments of reads (regions extracted from seeds) - not SW-aligning the whole read at once