Circlator

Fixes a bug where --assemble_not_only_assembler caused it to crash (issue 80).

Added options --fixstart_mincluster/--mincluster to change promer option -c|mincluster during fixstart stage.

- bug fix with regex not matching, so sequences lost, when running get_dnaa
- Update the built-in dna FASTA file from uniprot (issue 73)

- add --debug option to progcheck
- bug fix running spades (used to assume python2 was in path, but not any longer)
- drop dependency on bio_assembly_refinement python package
- add --verbose option to fixstart (see issue 57)
- bug fix handling whitespace in fasta headers with fixstart (see issue 64)
- bug fix incorrect break point coordinates in fixstart log

No changes to algorithm or final fasta. Cosmetic changes related to logging:
- bug fix reporting spades version (issue 56)
- more verbose reporting of version numbers (particularly python package dependencies)
- verbose added to bam2reads (issue 57)
- When verbose, output final summary of contig numbers and circularizations (issue 55)
- New option circlator all --unchanged_code, to let user choose return code when contigs unchanged (issue 55)

- options to not use the spades flags --careful (thanks again gedankenstuecke) or not use --only-assembler.
- new command "test", which does a complete run of "circlator all" on a small built-in test data set.