Added package (dependency definition) for freebayes-0.9.18
Committing freebayes 0.9.18. Removed direct access to command line. This will discontinue my own freebayes repo.
Update tool_dependencies.xml
Fixed a type and version strings mentioned by Nicola
Switches from sam_indices to fasta_indices.
Added bamleftalign to freebayes tool directory. Modified bamleftalign to accept fasta_indexes.loc. Added citation.
Removed tools/bamleftalign (it is now together with freebayes)
Merge pull request #33 from nekrut/feebayes_update

Update Freebayes suite.