use setStartCoordinate to comply with new interface
delete calls to set paralogy reversed
remove calls to setParseOffset as its no longer in api
return tokyo cabinet paths to build
convert iupac weirdo code letters to n and spit warning when converting sequences
Skip internal nodes properly in input trees in halAppendCactusSubtree.  They are not written because there is no sequence for them
Merge branch 'development' of github.com:glennhickey/cactus2hal into development
fix typo when converting lower-case special characters to n
merge development