fix Soap tests, add test for config file input
style fixes; relax transrate version
update version locks
generic subsampling now working
subsampling integrated with SOAPdenovo; biopsy dep updated
tests for Controller
Merge branch 'master' into soap

Conflicts:
	Gemfile.lock
	assemblotron.gemspec
moar tests
remove old constructors
inline documentation for all classes
don't store test-generated data
Merge branch 'master' of github.com:Blahah/assemblotron

Conflicts:
	test/data/subset.thousand_reads_l.fq
	test/data/subset.thousand_reads_r.fq
fix sample test
Merge branch 'master' of github.com:blahah/assemblotron into upstream

Conflicts:
	bin/atron
	lib/assemblotron.rb
	test/test_soap_denovo_trans.rb
enable writing when creating config file