Bugfixes with CD-hit and others

Fix cd-hit version check regexp - @tseemann
Fix issue #458 (cd-hit module)
Ensured only CDS features used, excluded ncRNAs
Updated deprecated calls in R scripts

Reduce minimum gene size

Reduce the minimum gene size filter from 120 to 18

Fix dependancy checking

Merge pull request #382 from andrewjpage/master

Fix dependancy checking option

Fix kraken-report and prank version finding

Merge pull request #379 from andrewjpage/version_fix

Version fix

Fix MAFFT and Kraken version finding

Fixes:
#360
#376

Bedtools getfasta fix

Merge pull request #374 from andrewjpage/bedtools_name

Bedtools getfasta format fix

Missing genes in core alignment represented as dashes not Ns

Merge pull request #358 from andrewjpage/dashes_for_missing

change missing gene in core to be dashes rather than Ns

Improve input file handling

Checks if an input FASTA file is actually a FASTA file.
Adds .gff extension if its not present (and it can be parsed as a GFF file).
Checks if the same GFF file has been provided twice by checking MD5. Only the first is used.
If duplicate IDs are found in any file, all gene IDs in the file are changed to MD5_index to avoid clashes.
Fix error getting MAFFT version string.
Dependancy versions for testing with Travis have been increased to latest.

Allow paralogs in core gene alignment

Merge pull request #343 from andrewjpage/core_paralogs

Optionally allow paralogs in core gene alignment

Allow for the MCL inflation value to be changed

v3.8.2

inflation value short