Removing more crufty files (stop committing them Miten!), making a bunch
of fixes.
Fixes
Merge remote-tracking branch 'origin/master'

Conflicts:
	nanopore/analyses/indels.py
	nanopore/analyses/substitutions.py
	testJobTree/environ.pickle
	testJobTree/jobs/t0/job
	testJobTree/jobs/t1/job
	testJobTree/jobs/t2/job
	testLog.txt
All working on tests
Merge remote-tracking branch 'origin/master'

Conflicts:
	nanopore/analyses/coverage.py
	nanopore/analyses/indels.py
	nanopore/analyses/kmerAnalysis.py
	nanopore/analyses/substitutions.py
	testJobTree/environ.pickle
	testLog.txt
Removing cruft