Iterator based parser and new gap detection algorithm

Created by: Piezoid

Uses a custom iterator for tokenizing the mapping files format. Getting rid of getline and istream_buf would be the next step, but would require custom buffer management. Maybe it's not worth it.

The main speed up is from a change in the gap detection algorithm. Instead of computing an histogram, mapping intervals are sorted then traversed with a min-queue holding the closing positions. That's a O(m) algorithm instead of a O(mn) algorithm (m: number of neighbours reads, n: read length)

The test suite fail because of the filtering bug you resolved. The validation results remains unchanged from master though.