add cores argument
update the test units
Opps, adding missing comma
Remote BLAST is run without the num_threads arg
If a string starts with double quotes, it ends with double quotes.

The bug was introduced in SHA: cdb0a2f9.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
change the --cores argument to --num_threads
Remove some dead code.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Refactoring - no need to use begin...end within method body.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
changing the cores variable to num_threads
Refactoring - be more expressive.

And add some FIXME annotations for later.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Merge pull request #49 from yeban/alpha

Minor refactoring and bug fixes.
merge upstream
Merge pull request #48 from IsmailM/add_cores_arg

Allows one to specify the number of threads to use
Merge https://github.com/monicadragan/GeneValidator into check_blast_path

Conflicts:
	bin/genevalidator
	lib/genevalidator/blast.rb
	lib/genevalidator/validation_alignment.rb
	lib/genevalidator/validation_duplication.rb
	lib/validation.rb
	test/test_all_validations.rb