bamcheck fix for projects with -d or -t in their path

[mp15]

Change bamcheck options so that targeted is passed via command line and not regexed out as this causes problems

[sb10]

Thanks for this Martin.

Do you know of a test script that utilises this code path, or can be easily made to do so?

Also, am I right in thinking that this change is backwards compatible in the sense that if an existing setup has '-d' in bamcheck_options, it will continue to work just fine?