Merge pull request #2 from percyfal/develop

Develop - misc updates
Fix bug where bwa.Aln erroneously classifies read 2 as read 1.
Merge branch 'master' into develop
Add documentation
Add docs
Add docs
Add documentation templates and functions for installing templates
Add sphinx.py
Add plot
First working draft of reporting ready
Merge branch 'feature/project_summary' into develop
Merge branch 'develop'
Add sorting of samples. Change pfx relpath
Partition subplot into several plots due to difficulties making plots fit
Make sure plot functions use correct number of samples
Add sequence census plot
Add HaloPlexCombine
Make PipedJobRunner use tmp output file names
Merge branch 'hotfix/piped_task_use_tmpfile'
Add determine_read_type function