add hal2fasta
add some gitignores
add read-only close to alignment interface
add some sandbox code in chain/ for building up browser support
add missing chain files
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