Closed issues:
- download_mlst_databases Could not connect to https://pubmlst.org/data/dbases.xml #77
- Something went wrong, got a 500 status code at /usr/local/share/perl/5.22.2/Bio/MLST/Download/Downloadable.pm line 24. #75
- Licence #68
- Issue with running get_sequence_type #65
Merged pull requests:
- Rt574328 readme #85 (ssjunnebo)
- add codecov #82 (ssjunnebo)
- fix typo in badge #81 (ssjunnebo)
- Add Docker badges to README.md #80 (ssjunnebo)
- include bioconda instructions #79 (ssjunnebo)
- 574328 fix readme #76 (ssjunnebo)
- update email address #74 (ssjunnebo)
- download from https #73 (andrewjpage)
- Update lustre directory in bin scripts #72 (vaofford)
- update 108 to 118 #71 (andrewjpage)
- Test descriptions #70 (andrewjpage)
- updates from review #69 (andrewjpage)
v2.1.1630910 (2016-11-04)
Merged pull requests:
- Update mlst to latest perl #67 (andrewjpage)
- Docker #66 (andrewjpage)
- nds change to dist zilla starter bundle #64 (nds)
- BUG: missing semicolon in get_emm_sequence_type script #63 (aslett1)
- Order alleles consistently when concatonating #62 (bewt85)
- Ignore metadata column headings in profiles #61 (bewt85)
- [468141,463456]: Cope better with small changes to alleles #60 (bewt85)
- Travis badge should just report master #59 (bewt85)
- Added AUTHORS with ap13 and bt5 as authors #58 (aslett1)
- BUG: Missing semicolon in get_sequence_type script #57 (bewt85)
- Ticket 463462: dodgy default arguments for blast_exec and makeblastdb_exec #56 (bewt85)
- Fix perl version in .travis.yml #55 (bewt85)
- Hopefully adds Travis CI support #54 (bewt85)
- Ticket 463083 Update versioning #53 (bewt85)
- Ticket 452414 Fix false contamination #52 (bewt85)
- Ticket 453529 Fix MLST spreadsheet output #51 (bewt85)
- Ticket 442599 Fix database updated #50 (bewt85)
- Fixes tests #49 (bewt85)
- Deal with cases where allele name contains a - or _ #48 (carlacummins)
- Prevented splitting of allele names in header #47 (carlacummins)
- pass in number of parallel processes #46 (andrewjpage)
- Added AUTHORS file #45 (aslett1)
- changes in main bin file due to addition of -md5 option in the lib #44 (jyothishnt)
- Changes in get_emm_sequence_type due to addition of -md5 option #43 (jyothishnt)
- Fixed error when using -a option #42 (carlacummins)
- Tests modified and passed successfully #41 (jyothishnt)
- New -md5 option #40 (jyothishnt)
last_reasonable_version (2014-05-15)
Merged pull requests:
- Improved error handling for unknown species #39 (carlacummins)
- Skip corrupt database #38 (andrewjpage)
- Updated sequence type choosing #37 (carlacummins)
- Edits to sequence type choosing #36 (carlacummins)
- output concat sequence where all are unknown #35 (andrewjpage)
- renamed LICENSE #34 (CraigPorter)
- GPL #33 (andrewjpage)
- filter out main allele #32 (andrewjpage)
- use new st #31 (andrewjpage)
- use st instead of gene id #30 (andrewjpage)
- When theres contamination allow for the alternative matches to be displayed in the results #29 (andrewjpage)
- make scripts executable #28 (andrewjpage)
- Emm st #27 (andrewjpage)
- added unit test for matching alleles with underscore eg S.pyogenes #26 (CraigPorter)
- ignore mlst clade for cdiff #25 (andrewjpage)
- filter underscores in header name #24 (andrewjpage)
- tests #23 (andrewjpage)
- Update documentation to work better with CPAN #22 (andrewjpage)
- Absent locus #21 (CraigPorter)
- Corrected bug in results filter for multiple species #20 (CraigPorter)
- Search multiple mlst #19 (CraigPorter)
- Check input fasta files exist. #18 (CraigPorter)
- allow multiple underscores and dashes in allele name #17 (andrewjpage)
- allow for underscores in allele name #16 (andrewjpage)
- docs #15 (andrewjpage)
- Phylip output support #14 (andrewjpage)
- Package up for CPAN #13 (andrewjpage)
- flag novel combinations #12 (andrewjpage)
- reverse complement #11 (andrewjpage)
- novel combinations #10 (andrewjpage)
- tmp dir in current working directory #9 (andrewjpage)
- try to fix broken input fastas and more overall tests #8 (andrewjpage)
- concat fasta sequences #7 (andrewjpage)
- mostly working for groups of files #6 (andrewjpage)
- default to base dir #5 (andrewjpage)
- tidy up #4 (andrewjpage)
- pull in databases from xml #3 (andrewjpage)
- full destination #2 (andrewjpage)
- initial build #1 (andrewjpage)