add masking and completely-unaligned sequence info
update to insertion stats & add the plot script

Requires R, ggplot2 and data.table.
Accidentally committed incomplete merge
add --minCovFrac to halLodInterpolate to control zoom-out clamping.  set fairly aggressively by default
Merge branch 'development' of https://github.com/glennhickey/hal
Merge branch 'master' of https://github.com/glennhickey/hal
Add -fPIC so that scripting languages can dlopen a hal library