First commit by js21. Added test to check if library_type option is working
Developing test
Developing test
Developing test
Developing test
Developing test
Developing test
New library_type flag has been implemented but one test is still failing.
added expected dir
All tests passed for the new implementation of the tophat mapper
Merge pull request #52 from js21/master

Tophat library_type options
Fixing bug RT:378950

Mainly fixed cmd/Common.pm. Used by all other modules, my top hat fix
was breaking other calls.
Added more tests to cope with the new tophat flags.
Merge pull request #53 from js21/fixing_snp_calling

Fixing bug RT:378950
Constraint on tophat library type

Validation of parameters passed to tophat  for a mapping run
Merge pull request #54 from js21/fixing_snp_calling

Constraint on tophat library type
time to localtime to give sensible, human readable values
Tests updated to take account of change from time to localtime in date of logs
Merge pull request #55 from aslett1/master

time to localtime to give sensible, human readable values
tests pass when config variable output order changes