BED feature

[isovic]

This PR adds a BED feature to polish only the specified regions of the input draft.
The feature is very useful when an assembly was patched (for example manually or by scaffolding), and the user wants to target only those regions instead of potentially disrupting an already high quality assembly.

One could suggest that instead of this feature the user should simply filter and clip overlaps from the outside, but that has a very nasty side-effect: since the region can begin at an arbitrary position (e.g. 1237bp in target), and the current windowing splits windows in fixed intervals (e.g. 500bp), that would mean that the first 237bp of the window where the region begins would have coverage 0x and the heuristics would kick in to trim the window. The end result would be a severely deteriorated assembly.
Another argument might be to turn off window trimming, but then internal windows would have plenty of insertions at their ends.

The only way around this is to implement a proper region-based polishing which generalizes to the full contig size as well as specified regions.

To implement this, some refactoring had to be done. Here is a brief description of work:

• The way breaking points were constructed had to be refactored because it was rigid (it expected that the polishing begins at coordinate 0 and would split the CIGAR in equally distant target coordinates), and entangled (it is not the responsibility of the Overlap class to find the CIGAR breakpoints).
• The Window class now stores both the start and end target coordinate of a window, which is very important to allow an arbitrary start/stop region for polishing. This feature will also be very useful in an unrelated upcoming feature.
• I added unit tests to verify that the breakpoint construction is good. Previously, this was untested, and there was a bug in the old logic. The new version seems to work properly.
• Added the BED parser, and unit tests to cover the code.

Both the regions and the windows may be of an arbitrary size.