remove chain stuf from dev branch.  now only in chains branch
add tosite method in columnIterator
try to speed up tosite
fix typos
add halAlignability tool to print simple alignability wiggles.  next step will be gerp-like conservation scores
make wig coordinates 1-based
fix --path option to sort genomes in path order
change --path into --span and --spanRoot
fix typos in doc
add getFullName method to sequence interface to give a UCSC style event.sequence name.  use this for maf output
fix brackets warning
oops
allow genome to be null in sequence for unit tests...
add bed targets option for hal2maf
stringstream error flags dont seem to do what they should.  work around
fix maf2hal to write proper sequence names.  ex a sequence name that was once dm3.chrX is now just chrx. the genome name remains dm3.
fix bug in halliftover where last column of interval skipped in loop
fix bug in hal2maf bed option
fix wrongful error on eof
Merge branch 'development' of github.com:glennhickey/hal into development