Merge pull request #40 from carlacummins/master

Updated prereqs to include java
Bug fix to stop dying when reference sequence provided by user
Merge pull request #41 from martinghunt/master

Bug fix to stop dying when reference sequence provided by user
update the default executable locations for the read correction and quasr
Merge pull request #42 from andrewjpage/update_manual_scripts_execs

update the default executable locations for the read correction and quasr
abs_path to inputs added