Merge master into mentalist_v0.2 (#26)

[dfornika]

• new script to filter Mentalist flag symbols from the calls

• Add .travis.yml file (Add .travis.yml file #18)

• Added travis.yml file

• Added 'Build Status' badge

• Update .travis.yml

• Update requirements for TravisCI testing

• kmer_class_for_locus function no longer exists

• Don't test on OS X

• Added coverage badge.

• Updated macOS install instructions

• Updated macOS install instructions

• Update README.md

• Update runtests.jl

• TravisCI testing on v0.5 is broken.

• Added <edam_operation> tag to 'mentalist call' galaxy tool (Added <edam_operation> tag to 'mentalist call' galaxy tool #21)

• fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases

• adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly

• new messages while loading a kmer db, better idea of how much each large step takes

• lots of new unit tests and a new fastq testing file. Coverage should be much higher now.

• Change version info for galaxy tools in master branch to 'master'

• support for analysing multiple samples

• reorganizing the argparse code and a bit of refactoring

• adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase

• small adjustment on a test

• Fix c_jejuni_fastq_file filename in test

• Adjusted kmer & vote numbers to match smaller test file.

• Update conda recipe

• Don't convert fasta_files paths to absolute paths (Don't convert fasta_files paths to absolute paths #23)

• Don't convert fasta_files paths to absolute paths

• Prepend database directory path on to relative paths for allele fasta files in db

• Don't create db_path variable, check for existence of fasta files

• Tidy up newlines

• Added test to check MLST calling after moving a database

• Relative paths in db (Relative paths in db #25)

• Don't convert fasta_files paths to absolute paths

• Prepend database directory path on to relative paths for allele fasta files in db

• Don't create db_path variable, check for existence of fasta files

• Tidy up newlines

• Added test to check MLST calling after moving a database

• Fixed issue with scheme fasta loading during calling

[coveralls]

Pull Request Test Coverage Report for Build 69

• 0 of 4 (0.0%) changed or added relevant lines in 2 files are covered.
• 70 unchanged lines in 2 files lost coverage.
• Overall coverage remained the same at 55.317%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/MentaLiST.jl	0	2	0.0%
src/calling_functions.jl	0	2	0.0%

Files with Coverage Reduction	New Missed Lines	%
src/MentaLiST.jl	1	0.0%
src/calling_functions.jl	69	61.11%

Totals
Change from base Build 64:	0.0%
Covered Lines:	463
Relevant Lines:	837

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💛 - Coveralls

[codecov-io]

Codecov Report

Merging #27 into master will not change coverage.
The diff coverage is 0%.

@@           Coverage Diff           @@
##           master      #27   +/-   ##
=======================================
  Coverage   55.31%   55.31%           
=======================================
  Files           5        5           
  Lines         837      837           
=======================================
  Hits          463      463           
  Misses        374      374

Impacted Files	Coverage Δ
src/MentaLiST.jl	0% <0%> (ø)	⬆️
src/calling_functions.jl	61.11% <0%> (ø)	⬆️

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