Merge pull request #4 from cancerit/dev

Pre-release 0.1
Merge pull request #9 from cancerit/dev

Ready for v1.0 and making public
Merge pull request #11 from cancerit/dev

Fixed #10, removed legacy test, and moved licence in setup.sh so it work...
Merge pull request #13 from cancerit/dev

v1.0.1 missing executables on install
Merge pull request #15 from cancerit/dev

Minor fix to readgroup id parsing
Merge pull request #20 from cancerit/dev

Pre-release 1.0.3
Merge pull request #21 from cancerit/dev

Silly mistake in unlink
Merge pull request #22 from cancerit/dev

Ready for Pancancer
Merge pull request #23 from cancerit/dev

threads wern't being honored when using process/index, bump version
Merge pull request #24 from cancerit/dev

Fixes for install and test warnings. Checked by JWH
Merge pull request #25 from cancerit/master

cleaning up merge commits