hack in halGetMaf to the C interface in chains
add file missing from last commit
move halBlockMapper from chain to liftover to break circular dependency created by adding maf function to chain
add missing include for frwite that causese error on hgwdev
add missing struct identifier to getMaf parameter which is needed by oldstyle C compilers
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
fix merge from dev
merge cmaf branch. kind of painful