Adding MSI

[jordiabante]

Garrett, the job is done here. However, along the way I found that informME_run always computes ESI and MC quantities. In fact, this is not a bug, I believe we deliberately got rid of the ESI and MC flags there. So I went ahead and followed the same logic with MSI. Also, right now, when generating the BED files, informME throws a terminal error in case the user passes the ESI/MSI/MC. Maybe we could just give the warning but keep on going with the rest? Anyways, before merging, maybe we can Skype and talk about it.

[jordiabante]

TODO:

• [x] Fix documentation flags (ESI,MSI,MC) in help files and README.
• [x] Improve handling of arguments by getopt and stderr messages.

[jordiabante]

TODO:

• [x] informME_run always computes ESI, MSI, and MC.
• [x] ESI/MSI/MC induce terminal error when making BED files?
• [x] Investigate wildcard in while loop.
• [x] Fix documentation flags (ESI,MSI,MC) in help files and README: do comp...

[jordiabante]

Alright, I went ahead and updated the PR with your suggestions. Let me know if there's anything else that you think could be improved!

[GarrettJenkinson]

Let's "take our own medicine" and have the toy example and submission scripts remove the "--" as well. For the toy model, it will allow us to test the usage we suggest. For the cluster scripts, we are providing these as template/examples on how we want people to use the software on their cluster.

[jordiabante]

TODO:

• [x] Garrett check.
• [x] Jordi human sample run.
• [x] John check.

[GarrettJenkinson]

I ran the toy model through my VM and everything looked good. I also updated the wiki to be a little more thorough about what to expect when doing a toy model. The remainder of the wiki can be updated once we tag v0.3.2.

[jordiabante]

Everything has been taken care of. Ready to merge to master.