CHANGELOG.md

+# Change Log
+
+## [Unreleased](https://github.com/sanger-pathogens/ariba/tree/HEAD)
+
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.1...HEAD)
+
+**Merged pull requests:**
+
+- Update python min version [\#247](https://github.com/sanger-pathogens/ariba/pull/247) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.13.1](https://github.com/sanger-pathogens/ariba/tree/v2.13.1) (2018-11-16)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.0...v2.13.1)
+
+**Closed issues:**
+
+- resfinder line breaks problem [\#236](https://github.com/sanger-pathogens/ariba/issues/236)
+
+**Merged pull requests:**
+
+- Include tb\_data dir in release [\#244](https://github.com/sanger-pathogens/ariba/pull/244) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.13.0](https://github.com/sanger-pathogens/ariba/tree/v2.13.0) (2018-11-16)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.12.1...v2.13.0)
+
+**Closed issues:**
+
+- Updated to 2.12.1 problems with resfinder [\#237](https://github.com/sanger-pathogens/ariba/issues/237)
+- Antibiotic resistance/susceptibility panel? [\#232](https://github.com/sanger-pathogens/ariba/issues/232)
+- Ariba fails when using virulencefinder db [\#216](https://github.com/sanger-pathogens/ariba/issues/216)
+- Ariba fails when using NFS directories for output [\#203](https://github.com/sanger-pathogens/ariba/issues/203)
+
+**Merged pull requests:**
+
+- Resfinder linebreaks [\#243](https://github.com/sanger-pathogens/ariba/pull/243) ([martinghunt](https://github.com/martinghunt))
+- Tb amr [\#242](https://github.com/sanger-pathogens/ariba/pull/242) ([martinghunt](https://github.com/martinghunt))
+- Do not use rmtree [\#235](https://github.com/sanger-pathogens/ariba/pull/235) ([martinghunt](https://github.com/martinghunt))
+- Add to codecov [\#234](https://github.com/sanger-pathogens/ariba/pull/234) ([ssjunnebo](https://github.com/ssjunnebo))
+- Include conda and docker badges [\#233](https://github.com/sanger-pathogens/ariba/pull/233) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.12.1](https://github.com/sanger-pathogens/ariba/tree/v2.12.1) (2018-06-15)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.12.0...v2.12.1)
+
+**Closed issues:**
+
+- PlasmidFinder databases have moved [\#218](https://github.com/sanger-pathogens/ariba/issues/218)
+- Add latest version of srst2\_argannot \(ARGannot\_r2.fasta\) [\#217](https://github.com/sanger-pathogens/ariba/issues/217)
+- Necessity of spades executable? [\#214](https://github.com/sanger-pathogens/ariba/issues/214)
+
+**Merged pull requests:**
+
+- Fix virulencefinder download [\#228](https://github.com/sanger-pathogens/ariba/pull/228) ([martinghunt](https://github.com/martinghunt))
+- Update docker image to Ubuntu 17.10 and Ariba v.2.12.0 [\#227](https://github.com/sanger-pathogens/ariba/pull/227) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.12.0](https://github.com/sanger-pathogens/ariba/tree/v2.12.0) (2018-05-13)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.11.1...v2.12.0)
+
+**Closed issues:**
+
+- Problems Task getref  xxxxFinder and CARD [\#211](https://github.com/sanger-pathogens/ariba/issues/211)
+
+**Merged pull requests:**
+
+- Remove spades warnings [\#224](https://github.com/sanger-pathogens/ariba/pull/224) ([martinghunt](https://github.com/martinghunt))
+- Get srst2\_argannot latest version r2 by default [\#223](https://github.com/sanger-pathogens/ariba/pull/223) ([martinghunt](https://github.com/martinghunt))
+- Getref xfinder bitbucket [\#222](https://github.com/sanger-pathogens/ariba/pull/222) ([martinghunt](https://github.com/martinghunt))
+- virulencefinder and nucmer version fixes [\#220](https://github.com/sanger-pathogens/ariba/pull/220) ([martinghunt](https://github.com/martinghunt))
+- change path to license file [\#219](https://github.com/sanger-pathogens/ariba/pull/219) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.11.1](https://github.com/sanger-pathogens/ariba/tree/v2.11.1) (2018-02-26)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.11.0-1...v2.11.1)
+
+**Merged pull requests:**
+
+- fix card db path [\#213](https://github.com/sanger-pathogens/ariba/pull/213) ([eppinglen](https://github.com/eppinglen))
+
+## [v2.11.0-1](https://github.com/sanger-pathogens/ariba/tree/v2.11.0-1) (2018-02-02)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.11.0...v2.11.0-1)
+
+## [v2.11.0](https://github.com/sanger-pathogens/ariba/tree/v2.11.0) (2018-02-02)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.10.4...v2.11.0)
+
+**Closed issues:**
+
+- micplot requires X window [\#176](https://github.com/sanger-pathogens/ariba/issues/176)
+
+**Merged pull requests:**
+
+- Option to use Spades and multithreading for Bowtie2 and Spades [\#210](https://github.com/sanger-pathogens/ariba/pull/210) ([andreyto](https://github.com/andreyto))
+
+## [v2.10.4](https://github.com/sanger-pathogens/ariba/tree/v2.10.4) (2018-02-01)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.10.3...v2.10.4)
+
+**Closed issues:**
+
+- Fails to getref card [\#206](https://github.com/sanger-pathogens/ariba/issues/206)
+
+**Merged pull requests:**
+
+- dont require X to run ariba [\#209](https://github.com/sanger-pathogens/ariba/pull/209) ([andrewjpage](https://github.com/andrewjpage))
+- update readme [\#208](https://github.com/sanger-pathogens/ariba/pull/208) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.10.3](https://github.com/sanger-pathogens/ariba/tree/v2.10.3) (2017-11-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.10.2...v2.10.3)
+
+**Closed issues:**
+
+- CARD downloads now bz2 [\#200](https://github.com/sanger-pathogens/ariba/issues/200)
+
+**Merged pull requests:**
+
+- Mlst hetmin bug [\#204](https://github.com/sanger-pathogens/ariba/pull/204) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.10.2](https://github.com/sanger-pathogens/ariba/tree/v2.10.2) (2017-11-08)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.10.1...v2.10.2)
+
+**Closed issues:**
+
+- The meaning of the flag "ref\_seq\_choose\_fail" [\#199](https://github.com/sanger-pathogens/ariba/issues/199)
+- How ariba deal with reads mapped to multiple clusters [\#198](https://github.com/sanger-pathogens/ariba/issues/198)
+- TypeError  [\#197](https://github.com/sanger-pathogens/ariba/issues/197)
+-  Test failures with bowtie2 2.3.2 [\#190](https://github.com/sanger-pathogens/ariba/issues/190)
+
+**Merged pull requests:**
+
+- Version bump 2.10.2 [\#202](https://github.com/sanger-pathogens/ariba/pull/202) ([martinghunt](https://github.com/martinghunt))
+- Changed card to utilise .tar.bz2 from .tar.gz [\#201](https://github.com/sanger-pathogens/ariba/pull/201) ([JezSw](https://github.com/JezSw))
+- correct spelling mistake [\#195](https://github.com/sanger-pathogens/ariba/pull/195) ([EdwardBetts](https://github.com/EdwardBetts))
+
+## [v2.10.1](https://github.com/sanger-pathogens/ariba/tree/v2.10.1) (2017-08-14)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.10.0...v2.10.1)
+
+**Closed issues:**
+
+- Creation of custom variant database containing indels, both in-frame or frameshifts  [\#189](https://github.com/sanger-pathogens/ariba/issues/189)
+- Clusters listed in debug.report.tsv not in report.tsv [\#188](https://github.com/sanger-pathogens/ariba/issues/188)
+- \_\_main\_\_ error message [\#187](https://github.com/sanger-pathogens/ariba/issues/187)
+- Failed Cluster [\#186](https://github.com/sanger-pathogens/ariba/issues/186)
+- What about MLST not hosted at pubmlst.org? [\#185](https://github.com/sanger-pathogens/ariba/issues/185)
+- How to detect presence or absence of a sequence carrying a deletion [\#184](https://github.com/sanger-pathogens/ariba/issues/184)
+
+**Merged pull requests:**
+
+- Add curl [\#194](https://github.com/sanger-pathogens/ariba/pull/194) ([martinghunt](https://github.com/martinghunt))
+- Bowtie2 version issues [\#193](https://github.com/sanger-pathogens/ariba/pull/193) ([martinghunt](https://github.com/martinghunt))
+- Fix utf-8 encoding problems [\#192](https://github.com/sanger-pathogens/ariba/pull/192) ([aunderwo](https://github.com/aunderwo))
+- Install specific release instead of master branch [\#191](https://github.com/sanger-pathogens/ariba/pull/191) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.10.0](https://github.com/sanger-pathogens/ariba/tree/v2.10.0) (2017-06-28)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.9.4...v2.10.0)
+
+**Closed issues:**
+
+- pubmlstget does not work with docker [\#180](https://github.com/sanger-pathogens/ariba/issues/180)
+- getref broken on CARD v1.1.8 [\#178](https://github.com/sanger-pathogens/ariba/issues/178)
+
+**Merged pull requests:**
+
+- Reviewer issues [\#182](https://github.com/sanger-pathogens/ariba/pull/182) ([martinghunt](https://github.com/martinghunt))
+- Task expandflag [\#181](https://github.com/sanger-pathogens/ariba/pull/181) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.9.4](https://github.com/sanger-pathogens/ariba/tree/v2.9.4) (2017-05-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.9.3...v2.9.4)
+
+**Closed issues:**
+
+- problems with fermilite [\#169](https://github.com/sanger-pathogens/ariba/issues/169)
+
+**Merged pull requests:**
+
+- Card 1.1.8 [\#179](https://github.com/sanger-pathogens/ariba/pull/179) ([martinghunt](https://github.com/martinghunt))
+- update AUTHORS and LICENSE [\#177](https://github.com/sanger-pathogens/ariba/pull/177) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v2.9.3](https://github.com/sanger-pathogens/ariba/tree/v2.9.3) (2017-04-28)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.9.2...v2.9.3)
+
+**Closed issues:**
+
+- Test failures with bowtie2 2.3.1 [\#170](https://github.com/sanger-pathogens/ariba/issues/170)
+
+**Merged pull requests:**
+
+- Getmlst dots in names [\#175](https://github.com/sanger-pathogens/ariba/pull/175) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.9.2](https://github.com/sanger-pathogens/ariba/tree/v2.9.2) (2017-04-27)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.9.1...v2.9.2)
+
+**Closed issues:**
+
+- Curious output [\#172](https://github.com/sanger-pathogens/ariba/issues/172)
+- How to input several fastq files for pooled assembly? [\#171](https://github.com/sanger-pathogens/ariba/issues/171)
+
+**Merged pull requests:**
+
+- Bowtie2.3.1 [\#174](https://github.com/sanger-pathogens/ariba/pull/174) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.9.1](https://github.com/sanger-pathogens/ariba/tree/v2.9.1) (2017-04-07)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.9.0...v2.9.1)
+
+**Closed issues:**
+
+- Failing to build wheel [\#168](https://github.com/sanger-pathogens/ariba/issues/168)
+- add VirulenceFinder [\#165](https://github.com/sanger-pathogens/ariba/issues/165)
+
+**Merged pull requests:**
+
+- Summary yes mutli het key error [\#173](https://github.com/sanger-pathogens/ariba/pull/173) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.9.0](https://github.com/sanger-pathogens/ariba/tree/v2.9.0) (2017-03-31)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.8.1...v2.9.0)
+
+**Closed issues:**
+
+- Ecoli no 1 profile warning [\#163](https://github.com/sanger-pathogens/ariba/issues/163)
+- Failed building wheel for ariba [\#161](https://github.com/sanger-pathogens/ariba/issues/161)
+- getref CARD  [\#160](https://github.com/sanger-pathogens/ariba/issues/160)
+
+**Merged pull requests:**
+
+- Summary read depth column [\#167](https://github.com/sanger-pathogens/ariba/pull/167) ([martinghunt](https://github.com/martinghunt))
+- new method \_get\_from\_virulencefinder [\#166](https://github.com/sanger-pathogens/ariba/pull/166) ([martinghunt](https://github.com/martinghunt))
+- Fix bug in README subheading rendering [\#164](https://github.com/sanger-pathogens/ariba/pull/164) ([fmaguire](https://github.com/fmaguire))
+
+## [v2.8.1](https://github.com/sanger-pathogens/ariba/tree/v2.8.1) (2017-03-04)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.7.2...v2.8.1)
+
+**Closed issues:**
+
+- compilation problem: ku128\_v \*r = &g-\>v.a\[idd\>\>1\].nei\[idd&1\]; [\#159](https://github.com/sanger-pathogens/ariba/issues/159)
+- error generating cluster [\#157](https://github.com/sanger-pathogens/ariba/issues/157)
+- --threads bug?  [\#155](https://github.com/sanger-pathogens/ariba/issues/155)
+
+**Merged pull requests:**
+
+- Mic plots [\#162](https://github.com/sanger-pathogens/ariba/pull/162) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.7.2](https://github.com/sanger-pathogens/ariba/tree/v2.7.2) (2017-02-02)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.7.1...v2.7.2)
+
+**Merged pull requests:**
+
+- Require pymummer 0.10.2 [\#158](https://github.com/sanger-pathogens/ariba/pull/158) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.7.1](https://github.com/sanger-pathogens/ariba/tree/v2.7.1) (2017-01-27)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.7.0...v2.7.1)
+
+**Merged pull requests:**
+
+- Newick rooting bug [\#156](https://github.com/sanger-pathogens/ariba/pull/156) ([martinghunt](https://github.com/martinghunt))
+- Check BeautifulSoup version number [\#154](https://github.com/sanger-pathogens/ariba/pull/154) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.7.0](https://github.com/sanger-pathogens/ariba/tree/v2.7.0) (2017-01-17)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.6.1...v2.7.0)
+
+**Merged pull requests:**
+
+- Add megares [\#153](https://github.com/sanger-pathogens/ariba/pull/153) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.6.1](https://github.com/sanger-pathogens/ariba/tree/v2.6.1) (2016-12-21)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.6.0...v2.6.1)
+
+**Merged pull requests:**
+
+- Ignore additional columns in MLST profiles [\#152](https://github.com/sanger-pathogens/ariba/pull/152) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.6.0](https://github.com/sanger-pathogens/ariba/tree/v2.6.0) (2016-12-20)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.5.1...v2.6.0)
+
+**Merged pull requests:**
+
+- Pubmlst [\#151](https://github.com/sanger-pathogens/ariba/pull/151) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.5.1](https://github.com/sanger-pathogens/ariba/tree/v2.5.1) (2016-12-05)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.5.0...v2.5.1)
+
+**Merged pull requests:**
+
+- Use flank length to choose best assembly [\#150](https://github.com/sanger-pathogens/ariba/pull/150) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.5.0](https://github.com/sanger-pathogens/ariba/tree/v2.5.0) (2016-11-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.4.0...v2.5.0)
+
+**Closed issues:**
+
+- broken link in the tarball hosted in pypi [\#147](https://github.com/sanger-pathogens/ariba/issues/147)
+
+**Merged pull requests:**
+
+- Ref seq choose use qry length [\#149](https://github.com/sanger-pathogens/ariba/pull/149) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.4.0](https://github.com/sanger-pathogens/ariba/tree/v2.4.0) (2016-11-01)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.3.0...v2.4.0)
+
+**Closed issues:**
+
+- Honour $TMPDIR for temporary files [\#143](https://github.com/sanger-pathogens/ariba/issues/143)
+- Report full codon change eg. AAT=\>AGG [\#142](https://github.com/sanger-pathogens/ariba/issues/142)
+- Report "partial" when 1 contig but not full gene [\#141](https://github.com/sanger-pathogens/ariba/issues/141)
+- Add --force to allow overwriting of output\_dir [\#138](https://github.com/sanger-pathogens/ariba/issues/138)
+- Report original names from gene database [\#136](https://github.com/sanger-pathogens/ariba/issues/136)
+- Cleanup after getref [\#135](https://github.com/sanger-pathogens/ariba/issues/135)
+
+**Merged pull requests:**
+
+- Consecutive genes fix [\#148](https://github.com/sanger-pathogens/ariba/pull/148) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.3.0](https://github.com/sanger-pathogens/ariba/tree/v2.3.0) (2016-10-12)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.5...v2.3.0)
+
+**Closed issues:**
+
+- Check minimap threads [\#144](https://github.com/sanger-pathogens/ariba/issues/144)
+
+**Merged pull requests:**
+
+- Torsten issues [\#146](https://github.com/sanger-pathogens/ariba/pull/146) ([martinghunt](https://github.com/martinghunt))
+- Report full codons and original sequence names [\#145](https://github.com/sanger-pathogens/ariba/pull/145) ([martinghunt](https://github.com/martinghunt))
+- Remove cdhit 2d [\#140](https://github.com/sanger-pathogens/ariba/pull/140) ([martinghunt](https://github.com/martinghunt))
+- Het snp bugs [\#139](https://github.com/sanger-pathogens/ariba/pull/139) ([martinghunt](https://github.com/martinghunt))
+- Docker installation [\#137](https://github.com/sanger-pathogens/ariba/pull/137) ([andrewjpage](https://github.com/andrewjpage))
+- Fix for download changes to resfinder data [\#134](https://github.com/sanger-pathogens/ariba/pull/134) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.5](https://github.com/sanger-pathogens/ariba/tree/v2.2.5) (2016-08-31)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.4...v2.2.5)
+
+**Merged pull requests:**
+
+- Bcftools ploidy [\#133](https://github.com/sanger-pathogens/ariba/pull/133) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.4](https://github.com/sanger-pathogens/ariba/tree/v2.2.4) (2016-08-23)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.3...v2.2.4)
+
+**Merged pull requests:**
+
+- Reportfilter bug [\#132](https://github.com/sanger-pathogens/ariba/pull/132) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.3](https://github.com/sanger-pathogens/ariba/tree/v2.2.3) (2016-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.2...v2.2.3)
+
+**Merged pull requests:**
+
+- bug fix summary when no samtools alt [\#131](https://github.com/sanger-pathogens/ariba/pull/131) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.2](https://github.com/sanger-pathogens/ariba/tree/v2.2.2) (2016-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.1...v2.2.2)
+
+**Merged pull requests:**
+
+- Contig renaming [\#130](https://github.com/sanger-pathogens/ariba/pull/130) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.1](https://github.com/sanger-pathogens/ariba/tree/v2.2.1) (2016-08-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.2.0...v2.2.1)
+
+**Merged pull requests:**
+
+- Aln2meta fix [\#129](https://github.com/sanger-pathogens/ariba/pull/129) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.2.0](https://github.com/sanger-pathogens/ariba/tree/v2.2.0) (2016-08-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.1.0...v2.2.0)
+
+**Merged pull requests:**
+
+- Version bump 2.2.0 [\#128](https://github.com/sanger-pathogens/ariba/pull/128) ([martinghunt](https://github.com/martinghunt))
+- summary no/NA consistency, phandango NAs [\#127](https://github.com/sanger-pathogens/ariba/pull/127) ([martinghunt](https://github.com/martinghunt))
+- Spaces in fasta headers [\#126](https://github.com/sanger-pathogens/ariba/pull/126) ([martinghunt](https://github.com/martinghunt))
+- Split show\_vars option into show\_known\_vars and show\_novel\_vars [\#125](https://github.com/sanger-pathogens/ariba/pull/125) ([martinghunt](https://github.com/martinghunt))
+- Bug fix reporting ref\_base\_assembled for a partial gene assembly [\#124](https://github.com/sanger-pathogens/ariba/pull/124) ([martinghunt](https://github.com/martinghunt))
+- When assembled is no, everything else should be no or NA [\#123](https://github.com/sanger-pathogens/ariba/pull/123) ([martinghunt](https://github.com/martinghunt))
+- Vfdb get full and core [\#122](https://github.com/sanger-pathogens/ariba/pull/122) ([martinghunt](https://github.com/martinghunt))
+- Add option to choose download version [\#121](https://github.com/sanger-pathogens/ariba/pull/121) ([martinghunt](https://github.com/martinghunt))
+- Summary improvements [\#120](https://github.com/sanger-pathogens/ariba/pull/120) ([martinghunt](https://github.com/martinghunt))
+- Allow fasta only to prepareref [\#119](https://github.com/sanger-pathogens/ariba/pull/119) ([martinghunt](https://github.com/martinghunt))
+- Add srst2 argannot [\#118](https://github.com/sanger-pathogens/ariba/pull/118) ([martinghunt](https://github.com/martinghunt))
+- Shorten filenames [\#117](https://github.com/sanger-pathogens/ariba/pull/117) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.1.0](https://github.com/sanger-pathogens/ariba/tree/v2.1.0) (2016-08-03)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.0.0...v2.1.0)
+
+**Merged pull requests:**
+
+- V2.0.0 bug fixes/improvements [\#116](https://github.com/sanger-pathogens/ariba/pull/116) ([martinghunt](https://github.com/martinghunt))
+- Het snp reporting [\#115](https://github.com/sanger-pathogens/ariba/pull/115) ([martinghunt](https://github.com/martinghunt))
+- Minor fixes [\#114](https://github.com/sanger-pathogens/ariba/pull/114) ([satta](https://github.com/satta))
+- Make sure c\*.h files included in distribution [\#113](https://github.com/sanger-pathogens/ariba/pull/113) ([martinghunt](https://github.com/martinghunt))
+
+## [v2.0.0](https://github.com/sanger-pathogens/ariba/tree/v2.0.0) (2016-07-29)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v1.0.1...v2.0.0)
+
+**Closed issues:**
+
+- report.tsv empty [\#96](https://github.com/sanger-pathogens/ariba/issues/96)
+
+**Merged pull requests:**
+
+- Update card version to 1.0.9 [\#112](https://github.com/sanger-pathogens/ariba/pull/112) ([martinghunt](https://github.com/martinghunt))
+- Tidy files [\#111](https://github.com/sanger-pathogens/ariba/pull/111) ([martinghunt](https://github.com/martinghunt))
+- Rename clusters [\#110](https://github.com/sanger-pathogens/ariba/pull/110) ([martinghunt](https://github.com/martinghunt))
+- End extend assemble flag bug [\#109](https://github.com/sanger-pathogens/ariba/pull/109) ([martinghunt](https://github.com/martinghunt))
+- Use fermilite [\#108](https://github.com/sanger-pathogens/ariba/pull/108) ([martinghunt](https://github.com/martinghunt))
+- General tidying [\#107](https://github.com/sanger-pathogens/ariba/pull/107) ([martinghunt](https://github.com/martinghunt))
+- Put -h option back for older python versions [\#106](https://github.com/sanger-pathogens/ariba/pull/106) ([martinghunt](https://github.com/martinghunt))
+- Use subcommands [\#105](https://github.com/sanger-pathogens/ariba/pull/105) ([martinghunt](https://github.com/martinghunt))
+- Check dendropy found and version ok [\#104](https://github.com/sanger-pathogens/ariba/pull/104) ([martinghunt](https://github.com/martinghunt))
+- Dendropy [\#103](https://github.com/sanger-pathogens/ariba/pull/103) ([martinghunt](https://github.com/martinghunt))
+- Minimap remove noise [\#102](https://github.com/sanger-pathogens/ariba/pull/102) ([martinghunt](https://github.com/martinghunt))
+-     Use minimap [\#101](https://github.com/sanger-pathogens/ariba/pull/101) ([martinghunt](https://github.com/martinghunt))
+- allow full VFDB to be downloaded [\#99](https://github.com/sanger-pathogens/ariba/pull/99) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.1](https://github.com/sanger-pathogens/ariba/tree/v1.0.1) (2016-06-28)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v1.0.0...v1.0.1)
+
+**Closed issues:**
+
+- Error running --test with CD-HIT and SPAdes [\#95](https://github.com/sanger-pathogens/ariba/issues/95)
+
+**Merged pull requests:**
+
+- Spades not untrusted [\#98](https://github.com/sanger-pathogens/ariba/pull/98) ([martinghunt](https://github.com/martinghunt))
+- add disclaimer to readme [\#97](https://github.com/sanger-pathogens/ariba/pull/97) ([martinghunt](https://github.com/martinghunt))
+- Add tmp dir description [\#94](https://github.com/sanger-pathogens/ariba/pull/94) ([martinghunt](https://github.com/martinghunt))
+- Make clearer that the env vars are exectuables, not dirs [\#93](https://github.com/sanger-pathogens/ariba/pull/93) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.0.0](https://github.com/sanger-pathogens/ariba/tree/v1.0.0) (2016-05-27)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/wip...v1.0.0)
+
+**Merged pull requests:**
+
+- Readme for 1.0.0 [\#92](https://github.com/sanger-pathogens/ariba/pull/92) ([martinghunt](https://github.com/martinghunt))
+- Phandango colours [\#91](https://github.com/sanger-pathogens/ariba/pull/91) ([martinghunt](https://github.com/martinghunt))
+- Group snps [\#90](https://github.com/sanger-pathogens/ariba/pull/90) ([martinghunt](https://github.com/martinghunt))
+- Only calculate half the matrix \(it's symmetric\) [\#89](https://github.com/sanger-pathogens/ariba/pull/89) ([martinghunt](https://github.com/martinghunt))
+- No attr assembly compare bug [\#88](https://github.com/sanger-pathogens/ariba/pull/88) ([martinghunt](https://github.com/martinghunt))
+- Vfdb names [\#87](https://github.com/sanger-pathogens/ariba/pull/87) ([martinghunt](https://github.com/martinghunt))
+- Say type is INT in the help [\#86](https://github.com/sanger-pathogens/ariba/pull/86) ([martinghunt](https://github.com/martinghunt))
+- Match gene ends [\#85](https://github.com/sanger-pathogens/ariba/pull/85) ([martinghunt](https://github.com/martinghunt))
+- Always report presabs vars [\#84](https://github.com/sanger-pathogens/ariba/pull/84) ([martinghunt](https://github.com/martinghunt))
+- Stop returning error when all clusters successful [\#83](https://github.com/sanger-pathogens/ariba/pull/83) ([martinghunt](https://github.com/martinghunt))
+- Tmp dir cleaning [\#82](https://github.com/sanger-pathogens/ariba/pull/82) ([martinghunt](https://github.com/martinghunt))
+- Die if spades error code is -7 [\#81](https://github.com/sanger-pathogens/ariba/pull/81) ([martinghunt](https://github.com/martinghunt))
+- Specify cdhit clusters [\#80](https://github.com/sanger-pathogens/ariba/pull/80) ([martinghunt](https://github.com/martinghunt))
+- Tmp dir option [\#79](https://github.com/sanger-pathogens/ariba/pull/79) ([martinghunt](https://github.com/martinghunt))
+- Bug fix with presets. Should be y/n not yes/no [\#78](https://github.com/sanger-pathogens/ariba/pull/78) ([martinghunt](https://github.com/martinghunt))
+- Update card from 1.0.5 to 1.0.6 [\#77](https://github.com/sanger-pathogens/ariba/pull/77) ([martinghunt](https://github.com/martinghunt))
+- Summary fixes [\#76](https://github.com/sanger-pathogens/ariba/pull/76) ([martinghunt](https://github.com/martinghunt))
+- Summary column control [\#75](https://github.com/sanger-pathogens/ariba/pull/75) ([martinghunt](https://github.com/martinghunt))
+- Minimise files [\#74](https://github.com/sanger-pathogens/ariba/pull/74) ([martinghunt](https://github.com/martinghunt))
+- Summary inconsistent bug [\#73](https://github.com/sanger-pathogens/ariba/pull/73) ([martinghunt](https://github.com/martinghunt))
+- bug fix, files were not being deleted [\#72](https://github.com/sanger-pathogens/ariba/pull/72) ([martinghunt](https://github.com/martinghunt))
+- Bug fix, now it actually deletes files as it goes [\#71](https://github.com/sanger-pathogens/ariba/pull/71) ([martinghunt](https://github.com/martinghunt))
+- Various fixes [\#70](https://github.com/sanger-pathogens/ariba/pull/70) ([martinghunt](https://github.com/martinghunt))
+- Various fixes [\#69](https://github.com/sanger-pathogens/ariba/pull/69) ([martinghunt](https://github.com/martinghunt))
+- Various fixes [\#68](https://github.com/sanger-pathogens/ariba/pull/68) ([martinghunt](https://github.com/martinghunt))
+- VFDB downloader [\#67](https://github.com/sanger-pathogens/ariba/pull/67) ([andrewjpage](https://github.com/andrewjpage))
+- Rename sequences [\#66](https://github.com/sanger-pathogens/ariba/pull/66) ([martinghunt](https://github.com/martinghunt))
+
+## [wip](https://github.com/sanger-pathogens/ariba/tree/wip) (2016-04-27)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.6.0...wip)
+
+**Implemented enhancements:**
+
+- Tests assume installed version of SPAdes [\#40](https://github.com/sanger-pathogens/ariba/issues/40)
+
+**Merged pull requests:**
+
+- Catch when no coverage from samtools [\#65](https://github.com/sanger-pathogens/ariba/pull/65) ([martinghunt](https://github.com/martinghunt))
+- Summary improvements [\#64](https://github.com/sanger-pathogens/ariba/pull/64) ([martinghunt](https://github.com/martinghunt))
+- Card rename [\#63](https://github.com/sanger-pathogens/ariba/pull/63) ([martinghunt](https://github.com/martinghunt))
+- Better cluster naming [\#62](https://github.com/sanger-pathogens/ariba/pull/62) ([martinghunt](https://github.com/martinghunt))
+- contig cov col report [\#61](https://github.com/sanger-pathogens/ariba/pull/61) ([martinghunt](https://github.com/martinghunt))
+- Catch when cannot determine insert size data [\#60](https://github.com/sanger-pathogens/ariba/pull/60) ([martinghunt](https://github.com/martinghunt))
+- Report all versions [\#59](https://github.com/sanger-pathogens/ariba/pull/59) ([martinghunt](https://github.com/martinghunt))
+- Bug fix with free text being put into more than one column [\#58](https://github.com/sanger-pathogens/ariba/pull/58) ([martinghunt](https://github.com/martinghunt))
+- Set nucmer opts to match nucmers defaults, but add --maxmatch [\#57](https://github.com/sanger-pathogens/ariba/pull/57) ([martinghunt](https://github.com/martinghunt))
+- New task prepareref [\#56](https://github.com/sanger-pathogens/ariba/pull/56) ([martinghunt](https://github.com/martinghunt))
+- Do not assume cluster representative comes first [\#55](https://github.com/sanger-pathogens/ariba/pull/55) ([martinghunt](https://github.com/martinghunt))
+- Card update use json [\#54](https://github.com/sanger-pathogens/ariba/pull/54) ([martinghunt](https://github.com/martinghunt))
+- Add files for TravisCI [\#53](https://github.com/sanger-pathogens/ariba/pull/53) ([martinghunt](https://github.com/martinghunt))
+- Phandango r bug [\#52](https://github.com/sanger-pathogens/ariba/pull/52) ([martinghunt](https://github.com/martinghunt))
+- Check all input files exist [\#51](https://github.com/sanger-pathogens/ariba/pull/51) ([martinghunt](https://github.com/martinghunt))
+- Bug in get one variant for one contig coding [\#50](https://github.com/sanger-pathogens/ariba/pull/50) ([martinghunt](https://github.com/martinghunt))
+- Check reads files exists before running pipeline [\#49](https://github.com/sanger-pathogens/ariba/pull/49) ([martinghunt](https://github.com/martinghunt))
+- Provide getref prefix to run [\#48](https://github.com/sanger-pathogens/ariba/pull/48) ([martinghunt](https://github.com/martinghunt))
+- Phandango fix [\#47](https://github.com/sanger-pathogens/ariba/pull/47) ([martinghunt](https://github.com/martinghunt))
+- Sample reads [\#46](https://github.com/sanger-pathogens/ariba/pull/46) ([martinghunt](https://github.com/martinghunt))
+- One thread not use multithreaded [\#45](https://github.com/sanger-pathogens/ariba/pull/45) ([martinghunt](https://github.com/martinghunt))
+- Make filtered report [\#44](https://github.com/sanger-pathogens/ariba/pull/44) ([martinghunt](https://github.com/martinghunt))
+- New task reportfilter [\#43](https://github.com/sanger-pathogens/ariba/pull/43) ([martinghunt](https://github.com/martinghunt))
+- Bux fix filtering rows [\#42](https://github.com/sanger-pathogens/ariba/pull/42) ([martinghunt](https://github.com/martinghunt))
+- Auto get ref genes, variant handling [\#41](https://github.com/sanger-pathogens/ariba/pull/41) ([martinghunt](https://github.com/martinghunt))
+- fix typo [\#39](https://github.com/sanger-pathogens/ariba/pull/39) ([satta](https://github.com/satta))
+- Implement multithreading [\#38](https://github.com/sanger-pathogens/ariba/pull/38) ([martinghunt](https://github.com/martinghunt))
+- Always run refcheck; Add JS candy output [\#37](https://github.com/sanger-pathogens/ariba/pull/37) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.6.0](https://github.com/sanger-pathogens/ariba/tree/v0.6.0) (2015-10-28)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.5.0...v0.6.0)
+
+**Merged pull requests:**
+
+- Improvements to summary output; new flag for non-synonymous variants [\#36](https://github.com/sanger-pathogens/ariba/pull/36) ([martinghunt](https://github.com/martinghunt))
+- Clarify usage: input must be tsv, not xls [\#35](https://github.com/sanger-pathogens/ariba/pull/35) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.5.0](https://github.com/sanger-pathogens/ariba/tree/v0.5.0) (2015-09-10)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.4.1...v0.5.0)
+
+**Merged pull requests:**
+
+- Various improvements [\#34](https://github.com/sanger-pathogens/ariba/pull/34) ([martinghunt](https://github.com/martinghunt))
+- Bug fix: refcheck now dies if spaces in sequence names [\#33](https://github.com/sanger-pathogens/ariba/pull/33) ([martinghunt](https://github.com/martinghunt))
+- Added AUTHORS with mh12 as author [\#32](https://github.com/sanger-pathogens/ariba/pull/32) ([aslett1](https://github.com/aslett1))
+
+## [v0.4.1](https://github.com/sanger-pathogens/ariba/tree/v0.4.1) (2015-07-14)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.4.0...v0.4.1)
+
+**Merged pull requests:**
+
+- Spades use untrusted-contigs [\#31](https://github.com/sanger-pathogens/ariba/pull/31) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.4.0](https://github.com/sanger-pathogens/ariba/tree/v0.4.0) (2015-06-10)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.3.2...v0.4.0)
+
+**Merged pull requests:**
+
+- Flag hit both strands [\#30](https://github.com/sanger-pathogens/ariba/pull/30) ([martinghunt](https://github.com/martinghunt))
+- Make cdhit optional [\#29](https://github.com/sanger-pathogens/ariba/pull/29) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.3.2](https://github.com/sanger-pathogens/ariba/tree/v0.3.2) (2015-05-12)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.3.1...v0.3.2)
+
+**Merged pull requests:**
+
+- Bug when samtools zero depth [\#28](https://github.com/sanger-pathogens/ariba/pull/28) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.3.1](https://github.com/sanger-pathogens/ariba/tree/v0.3.1) (2015-04-20)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.3.0...v0.3.1)
+
+**Merged pull requests:**
+
+- Bug fix aln score zero [\#27](https://github.com/sanger-pathogens/ariba/pull/27) ([martinghunt](https://github.com/martinghunt))
+- Bug fix getting read depth when there is an indel [\#26](https://github.com/sanger-pathogens/ariba/pull/26) ([martinghunt](https://github.com/martinghunt))
+- SSAPCE sd cannot exceed 1 [\#25](https://github.com/sanger-pathogens/ariba/pull/25) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.3.0](https://github.com/sanger-pathogens/ariba/tree/v0.3.0) (2015-04-07)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.2.0...v0.3.0)
+
+**Merged pull requests:**
+
+- Add test log file and do not gitignore .log files [\#24](https://github.com/sanger-pathogens/ariba/pull/24) ([martinghunt](https://github.com/martinghunt))
+- add option bowtie2\_preset; version bump [\#23](https://github.com/sanger-pathogens/ariba/pull/23) ([martinghunt](https://github.com/martinghunt))
+- Convert to uppercase [\#22](https://github.com/sanger-pathogens/ariba/pull/22) ([martinghunt](https://github.com/martinghunt))
+- Use bowtie2 [\#21](https://github.com/sanger-pathogens/ariba/pull/21) ([martinghunt](https://github.com/martinghunt))
+- Add ref alt read depth [\#20](https://github.com/sanger-pathogens/ariba/pull/20) ([martinghunt](https://github.com/martinghunt))
+- Report read counts [\#19](https://github.com/sanger-pathogens/ariba/pull/19) ([martinghunt](https://github.com/martinghunt))
+- Refcheck max length [\#18](https://github.com/sanger-pathogens/ariba/pull/18) ([martinghunt](https://github.com/martinghunt))
+- Make sspace and gapfiller optional [\#17](https://github.com/sanger-pathogens/ariba/pull/17) ([martinghunt](https://github.com/martinghunt))
+- write bad checked ref seqs to file; fix genetic\_code options [\#16](https://github.com/sanger-pathogens/ariba/pull/16) ([martinghunt](https://github.com/martinghunt))
+- Add summary task [\#15](https://github.com/sanger-pathogens/ariba/pull/15) ([martinghunt](https://github.com/martinghunt))
+- Check res genes [\#14](https://github.com/sanger-pathogens/ariba/pull/14) ([martinghunt](https://github.com/martinghunt))
+- Report percent identity and number bases assembled [\#13](https://github.com/sanger-pathogens/ariba/pull/13) ([martinghunt](https://github.com/martinghunt))
+- Use cd-hit-est [\#12](https://github.com/sanger-pathogens/ariba/pull/12) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.2.0](https://github.com/sanger-pathogens/ariba/tree/v0.2.0) (2015-02-20)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.1.2...v0.2.0)
+
+**Merged pull requests:**
+
+- Version 0.1.2 -\> 0.2.0 [\#11](https://github.com/sanger-pathogens/ariba/pull/11) ([martinghunt](https://github.com/martinghunt))
+- Use cdhit [\#10](https://github.com/sanger-pathogens/ariba/pull/10) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.1.2](https://github.com/sanger-pathogens/ariba/tree/v0.1.2) (2015-02-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.1.1...v0.1.2)
+
+**Merged pull requests:**
+
+- Bux fixes velvet path [\#9](https://github.com/sanger-pathogens/ariba/pull/9) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.1.1](https://github.com/sanger-pathogens/ariba/tree/v0.1.1) (2015-02-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.1.0...v0.1.1)
+
+**Merged pull requests:**
+
+- Update version to 0.1.1 [\#8](https://github.com/sanger-pathogens/ariba/pull/8) ([martinghunt](https://github.com/martinghunt))
+- Remove debugging sys.exit [\#7](https://github.com/sanger-pathogens/ariba/pull/7) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.1.0](https://github.com/sanger-pathogens/ariba/tree/v0.1.0) (2015-02-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v0.0.1...v0.1.0)
+
+**Merged pull requests:**
+
+- Move usage info to wiki [\#6](https://github.com/sanger-pathogens/ariba/pull/6) ([martinghunt](https://github.com/martinghunt))
+- fix executables and paths [\#5](https://github.com/sanger-pathogens/ariba/pull/5) ([martinghunt](https://github.com/martinghunt))
+- Fix bugs finding paths of dependencies [\#4](https://github.com/sanger-pathogens/ariba/pull/4) ([martinghunt](https://github.com/martinghunt))
+- Use spades [\#3](https://github.com/sanger-pathogens/ariba/pull/3) ([martinghunt](https://github.com/martinghunt))
+- Add velvet to dependencies [\#2](https://github.com/sanger-pathogens/ariba/pull/2) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.0.1](https://github.com/sanger-pathogens/ariba/tree/v0.0.1) (2015-02-12)
+**Merged pull requests:**
+
+- Initial working version [\#1](https://github.com/sanger-pathogens/ariba/pull/1) ([martinghunt](https://github.com/martinghunt))
+

README.md

@@ -60,7 +60,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions.
 If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/ariba/issues) or email us at ariba-help@sanger.ac.uk.
 
 ### Required dependencies
-  * [Python3][python] version >= 3.3.2
+  * [Python3][python] version >= 3.4.0
   * [Bowtie2][bowtie2] version >= 2.1.0
   * [CD-HIT][cdhit] version >= 4.6
   * [MUMmer][mummer] version >= 3.23
@@ -73,6 +73,7 @@ are not already installed:
   * pyfastaq >= 3.12.0
   * pysam >= 0.9.1
   * pymummer >= 0.10.1
+  * biopython
 
 ### Using pip3
 Install ARIBA using pip:

ariba/tb.py

@@ -212,8 +212,8 @@ def write_prepareref_metadata_file(mutations, outfile):
 
 def make_prepareref_files(outprefix):
     genbank_file = os.path.join(data_dir, 'NC_000962.3.gb')
-    mut_to_drug_json = os.path.join(data_dir, 'panel.20181115.json')
-    panel_txt_file = os.path.join(data_dir, 'panel.20181115.txt')
+    mut_to_drug_json = os.path.join(data_dir, 'panel.20181221.json')
+    panel_txt_file = os.path.join(data_dir, 'panel.20181221.txt')
     fasta_out = outprefix + '.fa'
     tsv_out = outprefix + '.tsv'
 

debian/changelog

+ariba (2.13.2+ds-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Sun, 23 Dec 2018 14:40:20 +0000
+
 ariba (2.13.1+ds-1) unstable; urgency=medium
 
   * New upstream release.

setup.py

@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.13.1',
+    version='2.13.2',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},