Add a setup script, to kick everything off

Depends on processing info from the LIMS.
Merge pull request #6 from fwip/master

Standardize nextseq Undetermined naming schema
Merge pull request #7 from fwip/generate_setup_script

Add a setup script, to kick everything off
Fix more density issues

The old way of calculating these was the correct one.  Also add
back in the id field so bed files are valid.