Circlator

- Supports samtools 1.2+ (thanks gedankenstuecke)
- Require pysam version 0.8.1-0.8.3 (latest 0.9.0 does not install with Travis)
- Added unit tests for the mapping code

Bug fix where circularization sometimes failed (thanks to Jia-Xing Yue for reporting)

Fixes bug when running the 'merge' task without --reads option (see issue 44).

- Add support for SPAdes version 3.6.2.
- Remove support for SPAdes 3.6.1 (but older versions are OK) because it does not output graph information.

- change to how SPAdes is run: instead of using the first kmer that returns a successful assembly, all kmers are tried and the one with the largest N50 is used. The old behaviour can be run with the option --assemble_spades_use_first
- clearer logging. --verbose is now just for debugging. Useful information for the user about how/why merges were (not) made is now only in the log files.
- ACT files written to compare SPAdes reassemblies against current state of the assembly. Useful for troubleshooting
- SPAdes version must be 3.5.0 or 3.6.0. Currently Circlator will not work with 3.6.1.