Revision history for HMMER2GO

Version	Date	Location
0.12	3/25/2015	Vancouver, BC

- Add compressed file support in the 'run' and 'getorf' command
  classes.
- Bugfixes for the latest GO mappings in the tests for the 'mapterms'
  command, and a minor fix in testing the output of the main command.

0.11	1/27/2015	Vancouver, BC

- Bugfix for the use of split in the mapterms command class.
  This fixes #4 on Github.

0.10	11/05/2014	Vancouver, BC

- Add methods to automatically retry attempts to fetch
  mapping file.

0.09	10/29/2014	Vancouver, BC

- Remove use of libwww in favor of net-ftp, which
  has no dependencies.
- Fix dependencies listed in cpanfile and Makefile.PL.

0.08	10/13/2014	Vancouver, BC

- Modify method for formatting HMM database to use core
  module (use 'File::Find' instead of 'File::Find::Rule'. The
  latter module is very good, it's just not a core module).

0.07	10/11/2014	Vancouver, BC

- Add method (and tests) for formatting custom HMM database for HMMER.
- Add better error handling and reporting when running HMMER.
- Add tests for running HMMER on custom DB created with 'pfamsearch'
  command.

0.06	10/03/2014	Vancouver, BC

- Add command for search Pfam for terms (called 'pfamsearch'),
  and create a database of HMMs from the search results, optionally.
- Add method to 'mapterms' class to get pfam to GO mapping file 
  automatically, thus avoiding the requirement for a user-supplied
  file.
- Change name of 'search' command to 'run' and add --program
  option to allow add more domin-finding methods in the future.

0.05	08/22/2014	Vancouver, BC

- Lower Perl version requirements to 5.10 (was 5.12).
- Expanded tests to cover newer (i.e., 5.20) and older (i.e,
  5.10) Perls.

0.04	08/20/2014	Vancouver, BC

- Fixed bug with not calculating the number of GO terms
  correctly (was underrepresenting the actual count).
- Fixed bug with GO description being truncated in the output.
- Removed use of UTF-8 characters for generating hash keys.
  - This resulted in speed improvements, and will allow the 
    Perl version requirement to be lowered in a future release.
- Add tests to make sure the correct results are reported when
  mapping GO terms, instead of just testing that there is 
  output.

0.03	08/01/2014	Vancouver, BC

- Add option to find all ORFs, not just the longest.
- Bug fixes to POD in several modules.
- Update Wiki and documentation for new option.

0.02	06/10/2014	Athens, GA

- Change name of 'fetch' command to 'fetchmap' to be
  more expressive.
- Make option to specify a file	mandatory for the
  'fetchmap' command so	there is a consist usage for
  all commands.
- Add documentation for main application.
- Add short option for getting documentation for all
  commands.

0.01    06/09/2014	Athens, GA

- Initial release.

