add --outPSL option to liftover.  writes 0s for cols 5 thru 8 since i dont understand them.
add missing tStart index to writePSL
store qSequence offset in psl extra struct.  use to make sure qStarts are written relative to sequence. fix bug where qBlock starts were mixed up between relative and absolute
use dcprobs to ensure that large sequence arrays get compressed.  hopefully speeds up browser
dont page 0 when creating a new array
change lod manager to always assume only lod 0 has sequence
add getAlignment method to genome interface
change genomes child cache to only load one genome at a time.  this is a tiny bit less efficeint since we reread all the childnames in a new vector each time.  but since opengenome can be so expensive in certain cases it is worth it
change spanning tree code in halcommon to use names instead of genome pointers when possible to avoid opening genomes that arent retunred
in mapped segment dont load genomes that may not be needed.  go through the alignment name interface instead
change getchildIndex to work with names instead of genome ptrs to avoid calling openGenome
move checking for sequence data to debug only
fix bug in last commit where getchildindex got totally broken
add validatePSL function to catch some basic errors
overhaul liftover especially block logic.  also fix psl.  add psl validator that will throw exception or assert if it sees a problem
some fixes for reverse strand coorsinates
add end postion to iterator print
Merge remote-tracking branch 'origin/chains' into liftover
pull apart dupes into different lines in psl