Added removeGenome and insertGenome methods
Merge branch 'development' of git://github.com/glennhickey/hal into development
ensure that all zero length sequences get added to both the position and the name cache (by storing them outside map)
remove some cruft
use columniterators tosite method to move around instead of creating new one each time.  not sure why this was taken out before. . hopefully i dont break anything
fix bug in last commit.  also scale probfrac when sequence length smaller than step
fix some checks on cahce size
fix bug in tosite where somehow the reference genome was incorrectly determined in weird cases
add some asserts
fix error when no sequence in genome.  this is a check that got broken in the v2 update
read in _totalSequenceLength from the sequence array if the DNA array is empty.  we want this to be valid even when the DNA is not stored to be consistent with last version
dont print empty sequences
add clearcache option to columniterators tosite method to guarantee that it lands on the desired column even in already visited.  update hallodgraph to use this option
Merge branch 'development' of github.com:glennhickey/hal into development
add lodchunk option
put chunk size back to default in hallodinterpolate
tone down prefetch to just root genomes
Merge branch 'development' of git@github.com:glennhickey/hal into development
hack bed reader to support rgb fields that are single number instread of three values
fix typo in last commit where itemb was getting wrong default