fix Makefile
comment assert that seems to have gone funny
try to fix asserts in getrange
add script that generates necessary files for assembly hub
add halTestGen to generate chains of events in hal
Merge branch 'development' of github.com:glennhickey/hal into development
rename makeAssemblyHub to hal2assembly hub, add copyright for ngan, put in makefile
add catch_all to block viz api try blocks
overhaul mapped segment sorting
finish segmented dups
revert back to first randgen code
fix hal2assemblyHub to skip genomes with zero sequence
merge blocks in blockmapper when possible.  cut out any mapbackc blocks that overlap existing blocks.  this is to close hole where we cut against flipset but add to mapsegs
change canAdd heuristic to use the highest delta in the column instead of the lowest.  also check agains half stepsize.
revise blockvis stuff to separate out mapped blocks with same query coordinates.  still needs work on edge cases
allow overlapping target paralogies for now.  will want to clip eventually
change halOpenLOD to accept .hal files too
fix c sequence buffer to not be 1 byte too short
add qChrom to dupe list structure
Merge commit 'origin/chains' into development