put check in runParallelShellCommands for empty list tho im not sure if this is the issue
fix bug in halAlignability and halPhyloPMain where more than the total length could be computed due to a bug in chopping into sequence coordinates
change recursive traversal in columnIterator and mappedSegment to not visit paralogy edges when parent genome is not within scope.  thus hopefully correcting a longstanding bug.
Added conservation track
Fix track labeling
Added bigBed indexing for searching function
Fixed indexing bug
Removed index of lifted-over bed tracks
change step parameter to scale in halLodExtract.  this way different subtrees can get different steps
add missing includes
Merge branch 'development' into lod

Conflicts:
	lod/halLodInterpolate.py
	lod/impl/halLodExtractMain.cpp
Index all annotation tracks including lifted-over tracks
fix typo in error message
Allow branch length updates
Merge branch 'development' of https://github.com/glennhickey/hal into development
Modularize and move hal2assemblyHub to assemblyHub directory
More refactoring. Also move annotation and alignment tracks into a composite track
fix slight issue with column count
Oops, nevermind, misunderstood the separators
Merge remote branch 'origin/development' into lod