Allow user to specify the negative control sample ID.

[dfornika]

We currently assume that the negative control sample has a filename that starts with NEG, and that no other sample in the run has a filename that starts with NEG. This is normally true, but may not be the case on every run.

Add a parameter --negative_control_samples that allows the user to specify the negative control sample ID.

[dfornika]

If possible, the user should be able to specify multiple negative control sample IDs.

[dfornika]

One additional requirement, to clarify:

If the user does not specify a --negative_control_samples flag, then the current behavior should be preserved. (Search for a sample that starts with NEG).