Bio-hansel

Fixes:

* incorrect order of parameters for BLAST against FASTA files.

Adds:
* `fastqsanger` to FASTQ regex
* coverage column for fastq input (`avg_tile_coverage` column)
* `--json` command-line option to output JSON representations of output files
* low coverage warning and test
* low coverage parameter

Developer:

* Using kwargs for table and json output.
* Beautifying IF Statements

README.rst fix

Fixes 27; QC check for unconfident results where downstream subtype tiles/kmers are missing so it's impossible to call subtype result unambiguously

Fixes:

- 25 Error in QC join function

Adds:
- `pyahocorasick` package for faster subtyping of reads and contigs using a Aho-Corasick Automaton
- Gzipped FASTA/FASTQ support

Fixes:
- 18; default to max-kmer=1000, min-kmer=8
- 21: QC functions no longer expect results from reads

Changes:
- command-line option for `--slow` run mode for `blastn` subtyping of contigs and Jellyfish k-mer count subtyping of reads
- Check external dependencies for `--slow` mode

Added:

- 14: QC methods for checking for mixed subtypes, intermediate subtypes, too many missing targets, ambiguous subtype result
- 13: technician friendly format (`-S`) with sample name, subtype result, QC status and QC messages
- `SubtypingParams` to hold QC and subtyping parameters like min k-mer threshold for subtype calling from reads and max missing tiles for QC
- added `qc_status` and `qc_messages` fields to regular summary output
- tests for QC


Fixed:

- check if output files exist, don't overwrite unless `--force` commandline option set


Changes:

- schemes can have scheme specific subtyping parameters (can add `SubtypingParams` object to scheme definition)
- updated tests