Update PairAligner_conf.pm

Added bidirectional netting functionality; a new flag set to zero by default. Added create_filter_duplicates node after netting.
Update EGPairAligner_conf.pm

Added bidirectional flag which is set to zero by default; Added create_filter_duplicates_net node in the workflow.
Update ParsePairAlignerConf.pm

If bidirectional_net flag is set to 1, Create the additional set of net jobs by swapping the reference and non-reference species. Then create the filter_duplicate_net jobs as they would be duplicates.
Merge pull request #4 from arnaudxk/master

Master