More documentation
Updated documentation
Added version to all scripts and modules
Fixed bug dealing with empty lines in a runfile. Removed -d option from demultiplex
No longer tries to set UID on files. Misc other fixes. Readme updates
Formatter ignores config entries for platforms unless they are _in_ _out_ formatted
Misc fixes
Misc fixes
Pulling in changes from origin
Merge remote-tracking branch 'origin/master'
Merged in new changes from dev
os.path.exists doesn't always work on symlinks
Ensure that ix_rename does not create broken links
Merge branch 'dev'
Added branch info to version
Added in functionality to mapSamples.py so that you can specify certain platforms to only include reads for

closes #1