maf tree WIP
fixed BedFormatError
hal2maf block trees mostly working

known bugs:
- ancestral references don't appear at top
- doesn't work correctly with restricting to a set of genomes / a
  subtree
Merge branch 'development' of https://github.com/glennhickey/hal
Merge branch 'development' of https://github.com/glennhickey/hal into development
Merge branch 'master' into development
add description to genomes.txt
add --topSegments and --bottomSegments options to halStats to print out segments in BED format
add test for DNA array presence to validate instead of crashing on LOD hals that have no DNA sequence info
mess of changes for safe copying of badly ordered genomes.
Start to separate up/down phases for segment mapping
Fix hal2maf block tree export on leaf insertions.
Fix prioritizing reference node at the wrong time.

This caused very small blocks with leaf references.
use parent as well as children in lod generation graph for an internal node.  also tweak some default parameter settings, boosting maxBlock and probeFrac, reducing minSequenceFrac and scaleCorFrac all to make lod geneation more sensitive
framework mostly there, but still a ways from working
Most existing unit tests passing.
Existing unit tests all pass.
Merge branch 'development' of github.com:glennhickey/hal into development
uncomment drawtree. add lod faq to hub readme.  use jobtree maxthreads for lod processes.  erase jobtree dir by default
fix bunch of crap broken in hal2assemblyHub.py options from my last commit