start integrating Melissas phyloP module
add enable def to compiler opts
rejig phylop build parameters to hopefully work on linux and mac.  some cleaning still needed
fix from melissa
test dir from melissa
make test.sh executable
reduce output float precision to 3
add coding style blurb
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
merge development
add --outPSL option to liftover.  writes 0s for cols 5 thru 8 since i dont understand them.
revamp hal2maf to use halBedScanner
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
add --baseComp option to halStats
add option to copy the halfile to the assemblyhub outdir