BED file coordinates should be treated as 0-start, half-open intervals

[huddlej]

Current Behavior

augur's functions to read in BED files with a CSV parser treat coordinates as 0-start, fully-closed intervals. This means they include both the start and the end coordinates in the interval and treat these as zero-based coordinates. This behavior happens in load_excluded_sites in tree.py and also in augur mask.

The current behavior results in one extra base getting included at the end of given interval.

Expected behavior

BED coordinates should be 0-start, half-open intervals.

Possible solution

• Update BED functions to not add 1 to the final coordinate of each range
• Update corresponding BED files in test data and production builds to the desired coordinates under the expected BED coordinate behavior

[jstoja]

I've taken a shot at it with #521 but I didn't find any BED files for excluded_sites.