add allSeqeunces option.  dont sample small sequences.  todo -- make sure this doesnt break writing
dont sample every sequence unless allSequences flag is set. unsampled sequences are now set to unaligned blocks
remove extraneous simcolon
replace first line in lod.txt to contain relative path to localHalFile
expose maxBlock, scale and maxDNA options from halLodInterpolate.py in hal2assemblyHub.py
Merge branch 'development' into liftover
refactor block mapper a little to share some code with liftover