Establish working dir and prefix earlier in __call__
updated comment
Correct documentation of --header_id_regex option to RTAX.
Correct documentation of --read_id_regex and --header_id_regex options to RTAX.
added non list lookups
missed one lookup
Merge pull request #1056 from wasade/parallel_wrapper_tweaks

Establish working dir and prefix earlier in __call__
Merge pull request #1080 from davidsoergel/master

Correct documentation of --read_id_regex and --header_id_regex options to RTAX.
Merge pull request #1088 from wasade/issue_1087

added non list lookups