Optimize the speed of genotyping when some sites have very high coverage (>500M bases). Now sub-sampling to keep a random set of 10,000 bases for such sites.
Add two methods to AlignmentReader to determine the minimum and maximum genomic locations represented in the reader. This is useful when suggesting slices to split a set of alignments. This commit includes a fix for possible null start or end positions in slices generated with suggest-position-slices.
One last optimization. This version now has constant speed irrespective of the time it has been running.
Merge branch 'stable' of https://github.com/CampagneLaboratory/goby into stable