Merge master into mentalist_v0.2 (#26) (#27)

* Merge master into mentalist_v0.2 (#26)

* new script to filter Mentalist flag symbols from the calls

* 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 (#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 (#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 (#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

* Merge master into mentalist_v0.2 (#28)

* new script to filter Mentalist flag symbols from the calls

* 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 (#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 (#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 (#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