remove cout
add cleanResults function to cut off gaps between first and last blocks and to make sure the output thickstartend is the same as chrom startend
activate reverse orgin support for mapped segemnt for liftover. hope it works
revise rearrangement to prioritize duplication events so they dont get mislabled transpositions or inversions.  also use the canonical paralog notion when iding dupes.
revise parallel hal2maf interface to be simpler
fix autoslice rounding
update readme and to version 1.4
add coding style blurb
fix bug in liftover makefile that didnt notice until doing fresh clone
Merge branch 'master' into development
update processing of halStats --genomes to reflect that list returned is not comma separated due to latest git merge.  should eventually replace with the halStats.py methods
update getHalGenomes to reflect commaless output of halStats which got replaced in merge confusion
clean up printing code a bit.  no goes through print interface for segments
filter out lines with zero blocks when writing bed12