v2.14.6 (2020-09-07)
Closed issues:
- PubMLST URL change breaks pubmlstget #304
- get_ref card is attempting to download RGI #301
- Reference dataset of megares cannot be downloaded #287
Merged pull requests:
- Fix for changes in PubMLST url #305 (rpetit3)
- Solution 1: for fixing CARD download #302 (rpetit3)
- Update CARD citation message #289 (fmaguire)
v2.14.5 (2020-05-14)
Closed issues:
- Megares Downloading Error #294
- Summarising MLST reports? #292
- CARD 3.0.6 introduces white space in seq id causing fasta/metadata mismatch #284
- ARGannot download fails #281
Merged pull requests:
- bump version number #297 (puethe)
- Handle megares 2.0.0 #295 (martinghunt)
- Correct swapped col and row filters #288 (aunderwo)
- Remove support information #286 (kpepper)
v2.14.4 (2019-09-24)
Merged pull requests:
v2.14.3 (2019-08-30)
Closed issues:
- Version 3.0.3 of CARD breaks prepareref #278
- matplotlib listed twice as a dep in setup.py #275
- v2.14.1 attributeError: 'Namespace' object has no attribute 'cdhit_max_memory' #273
- Use ariba run for several isolates in batch #262
- Stopping! Signal received: 13 #238
Merged pull requests:
- Added default locale to docker file #280 (kpepper)
- Fix for issue #278 Version 3.0.3 of CARD breaks prepareref #279 (kpepper)
- Remove extra matplotlib entry in install_requires #277 (andersgs)
- Removed the specific Ariba release number from the docker file #276 (kpepper)
v2.14.2 (2019-06-21)
Fixed bugs:
- Issue with ariba and slurm (signal 18, signal 20) #263
Merged pull requests:
- RT 660940 - add spades to docker file #274 (kpepper)
- Added AUTHORS and LICENSE to the manifest #272 (kpepper)
v2.14.1 (2019-06-13)
Merged pull requests:
v2.14.0 (2019-06-06)
Closed issues:
- Reference dataset of ARG-ANNOT cannot be downloaded #265
- unable to download mlst schemes #264
- Several "At least one cluster failed!Stopping..." errors #261
- Allow increasing cd-hit-est memory allocation #255
- Ariba pubmlstget Error #240
- segmentation fault when I import ariba #230
- How to use spades and set minimum coverage #215
Merged pull requests:
- Additional v2.14.0 updates #270 (kpepper)
- Added getref feature for NCBI's Bacterial Antimicrobial Resistance Reference Gene Database #269 (schultzm)
v2.13.5 (2019-03-26)
Fixed bugs:
- Ariba fails without --noclean depending on database #205
Closed issues:
- Installation failed: clang: error: linker command failed with exit code 1 (use -v to see invocation) #245
- virfinddb db not downloading properly #229
- getref error with resfinder db #225
Merged pull requests:
- Updated CHANGELOG.md #260 (kpepper)
- Bump version to 2.13.5 and fix Spades invocation issue #259 (kpepper)
- Minor code change to mitigate issue #245 (installation failure) #258 (kpepper)
v2.13.4 (2019-03-15)
Closed issues:
Merged pull requests:
- Rebuilt CHANGELOG for v2.13.4 #257 (kpepper)
- Allow increasing cd-hit-est memory allocation #255 #256 (kpepper)
v2.13.3 (2019-01-02)
Merged pull requests:
- TB D94A fix #251 (martinghunt)
v2.13.2 (2018-12-21)
Merged pull requests:
- Update tb panel #250 (martinghunt)
- Added changelog #248 (ssjunnebo)
- Update python min version #247 (ssjunnebo)
v2.13.1 (2018-11-16)
Closed issues:
- resfinder line breaks problem #236
Merged pull requests:
- Include tb_data dir in release #244 (martinghunt)
v2.13.0 (2018-11-16)
Closed issues:
- Updated to 2.12.1 problems with resfinder #237
- Antibiotic resistance/susceptibility panel? #232
- Ariba fails when using virulencefinder db #216
- Ariba fails when using NFS directories for output #203
Merged pull requests:
- Resfinder linebreaks #243 (martinghunt)
- Tb amr #242 (martinghunt)
- Do not use rmtree #235 (martinghunt)
- Add to codecov #234 (ssjunnebo)
- Include conda and docker badges #233 (ssjunnebo)
v2.12.1 (2018-06-15)
Closed issues:
- PlasmidFinder databases have moved #218
- Add latest version of srst2_argannot (ARGannot_r2.fasta) #217
- Necessity of spades executable? #214
Merged pull requests:
- Fix virulencefinder download #228 (martinghunt)
- Update docker image to Ubuntu 17.10 and Ariba v.2.12.0 #227 (ssjunnebo)
v2.12.0 (2018-05-13)
Closed issues:
- Problems Task getref xxxxFinder and CARD #211
Merged pull requests:
- Remove spades warnings #224 (martinghunt)
- Get srst2_argannot latest version r2 by default #223 (martinghunt)
- Getref xfinder bitbucket #222 (martinghunt)
- virulencefinder and nucmer version fixes #220 (martinghunt)
- change path to license file #219 (ssjunnebo)
v2.11.1 (2018-02-26)
Merged pull requests:
v2.11.0-1 (2018-02-02)
v2.11.0 (2018-02-02)
Closed issues:
- micplot requires X window #176
Merged pull requests:
v2.10.4 (2018-02-01)
Closed issues:
- Fails to getref card #206
Merged pull requests:
- dont require X to run ariba #209 (andrewjpage)
- update readme #208 (ssjunnebo)
v2.10.3 (2017-11-24)
Closed issues:
- CARD downloads now bz2 #200
Merged pull requests:
- Mlst hetmin bug #204 (martinghunt)
v2.10.2 (2017-11-08)
Closed issues:
- The meaning of the flag "ref_seq_choose_fail" #199
- How ariba deal with reads mapped to multiple clusters #198
- TypeError #197
- Test failures with bowtie2 2.3.2 #190
Merged pull requests:
- Version bump 2.10.2 #202 (martinghunt)
- Changed card to utilise .tar.bz2 from .tar.gz #201 (JezSw)
- correct spelling mistake #195 (EdwardBetts)
v2.10.1 (2017-08-14)
Closed issues:
- Creation of custom variant database containing indels, both in-frame or frameshifts #189
- Clusters listed in debug.report.tsv not in report.tsv #188
- __main__ error message #187
- Failed Cluster #186
- What about MLST not hosted at pubmlst.org? #185
- How to detect presence or absence of a sequence carrying a deletion #184
Merged pull requests:
- Add curl #194 (martinghunt)
- Bowtie2 version issues #193 (martinghunt)
- Fix utf-8 encoding problems #192 (aunderwo)
- Install specific release instead of master branch #191 (martinghunt)
v2.10.0 (2017-06-28)
Closed issues:
Merged pull requests:
- Reviewer issues #182 (martinghunt)
- Task expandflag #181 (martinghunt)
v2.9.4 (2017-05-24)
Closed issues:
- problems with fermilite #169
Merged pull requests:
- Card 1.1.8 #179 (martinghunt)
- update AUTHORS and LICENSE #177 (ssjunnebo)
v2.9.3 (2017-04-28)
Closed issues:
- Test failures with bowtie2 2.3.1 #170
Merged pull requests:
- Getmlst dots in names #175 (martinghunt)
v2.9.2 (2017-04-27)
Closed issues:
Merged pull requests:
- Bowtie2.3.1 #174 (martinghunt)
v2.9.1 (2017-04-07)
Closed issues:
Merged pull requests:
- Summary yes mutli het key error #173 (martinghunt)
v2.9.0 (2017-03-31)
Closed issues:
Merged pull requests:
- Summary read depth column #167 (martinghunt)
- new method _get_from_virulencefinder #166 (martinghunt)
- Fix bug in README subheading rendering #164 (fmaguire)
v2.8.1 (2017-03-04)
Closed issues:
- compilation problem: ku128_v *r = &g->v.a[idd>>1].nei[idd&1]; #159
- error generating cluster #157
- --threads bug? #155
Merged pull requests:
- Mic plots #162 (martinghunt)
v2.7.2 (2017-02-02)
Merged pull requests:
- Require pymummer 0.10.2 #158 (martinghunt)
v2.7.1 (2017-01-27)
Merged pull requests:
- Newick rooting bug #156 (martinghunt)
- Check BeautifulSoup version number #154 (martinghunt)
v2.7.0 (2017-01-17)
Merged pull requests:
- Add megares #153 (martinghunt)
v2.6.1 (2016-12-21)
Merged pull requests:
- Ignore additional columns in MLST profiles #152 (andrewjpage)
v2.6.0 (2016-12-20)
Merged pull requests:
- Pubmlst #151 (martinghunt)
v2.5.1 (2016-12-05)
Merged pull requests:
- Use flank length to choose best assembly #150 (martinghunt)
v2.5.0 (2016-11-18)
Closed issues:
- broken link in the tarball hosted in pypi #147
Merged pull requests:
- Ref seq choose use qry length #149 (martinghunt)
v2.4.0 (2016-11-01)
Closed issues:
- Honour $TMPDIR for temporary files #143
- Report full codon change eg. AAT=>AGG #142
- Report "partial" when 1 contig but not full gene #141
- Add --force to allow overwriting of output_dir #138
- Report original names from gene database #136
- Cleanup after getref #135
Merged pull requests:
- Consecutive genes fix #148 (martinghunt)
v2.3.0 (2016-10-12)
Closed issues:
- Check minimap threads #144
Merged pull requests:
- Torsten issues #146 (martinghunt)
- Report full codons and original sequence names #145 (martinghunt)
- Remove cdhit 2d #140 (martinghunt)
- Het snp bugs #139 (martinghunt)
- Docker installation #137 (andrewjpage)
- Fix for download changes to resfinder data #134 (martinghunt)
v2.2.5 (2016-08-31)
Merged pull requests:
- Bcftools ploidy #133 (martinghunt)
v2.2.4 (2016-08-23)
Merged pull requests:
- Reportfilter bug #132 (martinghunt)
v2.2.3 (2016-08-22)
Merged pull requests:
- bug fix summary when no samtools alt #131 (martinghunt)
v2.2.2 (2016-08-22)
Merged pull requests:
- Contig renaming #130 (martinghunt)
v2.2.1 (2016-08-18)
Merged pull requests:
- Aln2meta fix #129 (martinghunt)
v2.2.0 (2016-08-18)
Merged pull requests:
- Version bump 2.2.0 #128 (martinghunt)
- summary no/NA consistency, phandango NAs #127 (martinghunt)
- Spaces in fasta headers #126 (martinghunt)
- Split show_vars option into show_known_vars and show_novel_vars #125 (martinghunt)
- Bug fix reporting ref_base_assembled for a partial gene assembly #124 (martinghunt)
- When assembled is no, everything else should be no or NA #123 (martinghunt)
- Vfdb get full and core #122 (martinghunt)
- Add option to choose download version #121 (martinghunt)
- Summary improvements #120 (martinghunt)
- Allow fasta only to prepareref #119 (martinghunt)
- Add srst2 argannot #118 (martinghunt)
- Shorten filenames #117 (martinghunt)
v2.1.0 (2016-08-03)
Merged pull requests:
- V2.0.0 bug fixes/improvements #116 (martinghunt)
- Het snp reporting #115 (martinghunt)
- Minor fixes #114 (satta)
- Make sure c*.h files included in distribution #113 (martinghunt)
v2.0.0 (2016-07-29)
Closed issues:
- report.tsv empty #96
Merged pull requests:
- Update card version to 1.0.9 #112 (martinghunt)
- Tidy files #111 (martinghunt)
- Rename clusters #110 (martinghunt)
- End extend assemble flag bug #109 (martinghunt)
- Use fermilite #108 (martinghunt)
- General tidying #107 (martinghunt)
- Put -h option back for older python versions #106 (martinghunt)
- Use subcommands #105 (martinghunt)
- Check dendropy found and version ok #104 (martinghunt)
- Dendropy #103 (martinghunt)
- Minimap remove noise #102 (martinghunt)
-
Use minimap [\#101](https://github.com/sanger-pathogens/ariba/pull/101) ([martinghunt](https://github.com/martinghunt)) - allow full VFDB to be downloaded #99 (andrewjpage)
v1.0.1 (2016-06-28)
Closed issues:
- Error running --test with CD-HIT and SPAdes #95
Merged pull requests:
- Spades not untrusted #98 (martinghunt)
- add disclaimer to readme #97 (martinghunt)
- Add tmp dir description #94 (martinghunt)
- Make clearer that the env vars are exectuables, not dirs #93 (martinghunt)
v1.0.0 (2016-05-27)
Merged pull requests:
- Readme for 1.0.0 #92 (martinghunt)
- Phandango colours #91 (martinghunt)
- Group snps #90 (martinghunt)
- Only calculate half the matrix (it's symmetric) #89 (martinghunt)
- No attr assembly compare bug #88 (martinghunt)
- Vfdb names #87 (martinghunt)
- Say type is INT in the help #86 (martinghunt)
- Match gene ends #85 (martinghunt)
- Always report presabs vars #84 (martinghunt)
- Stop returning error when all clusters successful #83 (martinghunt)
- Tmp dir cleaning #82 (martinghunt)
- Die if spades error code is -7 #81 (martinghunt)
- Specify cdhit clusters #80 (martinghunt)
- Tmp dir option #79 (martinghunt)
- Bug fix with presets. Should be y/n not yes/no #78 (martinghunt)
- Update card from 1.0.5 to 1.0.6 #77 (martinghunt)
- Summary fixes #76 (martinghunt)
- Summary column control #75 (martinghunt)
- Minimise files #74 (martinghunt)
- Summary inconsistent bug #73 (martinghunt)
- bug fix, files were not being deleted #72 (martinghunt)
- Bug fix, now it actually deletes files as it goes #71 (martinghunt)
- Various fixes #70 (martinghunt)
- Various fixes #69 (martinghunt)
- Various fixes #68 (martinghunt)
- VFDB downloader #67 (andrewjpage)
- Rename sequences #66 (martinghunt)
wip (2016-04-27)
Implemented enhancements:
- Tests assume installed version of SPAdes #40
Merged pull requests:
- Catch when no coverage from samtools #65 (martinghunt)
- Summary improvements #64 (martinghunt)
- Card rename #63 (martinghunt)
- Better cluster naming #62 (martinghunt)
- contig cov col report #61 (martinghunt)
- Catch when cannot determine insert size data #60 (martinghunt)
- Report all versions #59 (martinghunt)
- Bug fix with free text being put into more than one column #58 (martinghunt)
- Set nucmer opts to match nucmers defaults, but add --maxmatch #57 (martinghunt)
- New task prepareref #56 (martinghunt)
- Do not assume cluster representative comes first #55 (martinghunt)
- Card update use json #54 (martinghunt)
- Add files for TravisCI #53 (martinghunt)
- Phandango r bug #52 (martinghunt)
- Check all input files exist #51 (martinghunt)
- Bug in get one variant for one contig coding #50 (martinghunt)
- Check reads files exists before running pipeline #49 (martinghunt)
- Provide getref prefix to run #48 (martinghunt)
- Phandango fix #47 (martinghunt)
- Sample reads #46 (martinghunt)
- One thread not use multithreaded #45 (martinghunt)
- Make filtered report #44 (martinghunt)
- New task reportfilter #43 (martinghunt)
- Bux fix filtering rows #42 (martinghunt)
- Auto get ref genes, variant handling #41 (martinghunt)
- fix typo #39 (satta)
- Implement multithreading #38 (martinghunt)
- Always run refcheck; Add JS candy output #37 (martinghunt)
v0.6.0 (2015-10-28)
Merged pull requests:
- Improvements to summary output; new flag for non-synonymous variants #36 (martinghunt)
- Clarify usage: input must be tsv, not xls #35 (martinghunt)
v0.5.0 (2015-09-10)
Merged pull requests:
- Various improvements #34 (martinghunt)
- Bug fix: refcheck now dies if spaces in sequence names #33 (martinghunt)
- Added AUTHORS with mh12 as author #32 (aslett1)
v0.4.1 (2015-07-14)
Merged pull requests:
- Spades use untrusted-contigs #31 (martinghunt)
v0.4.0 (2015-06-10)
Merged pull requests:
- Flag hit both strands #30 (martinghunt)
- Make cdhit optional #29 (martinghunt)
v0.3.2 (2015-05-12)
Merged pull requests:
- Bug when samtools zero depth #28 (martinghunt)
v0.3.1 (2015-04-20)
Merged pull requests:
- Bug fix aln score zero #27 (martinghunt)
- Bug fix getting read depth when there is an indel #26 (martinghunt)
- SSAPCE sd cannot exceed 1 #25 (martinghunt)
v0.3.0 (2015-04-07)
Merged pull requests:
- Add test log file and do not gitignore .log files #24 (martinghunt)
- add option bowtie2_preset; version bump #23 (martinghunt)
- Convert to uppercase #22 (martinghunt)
- Use bowtie2 #21 (martinghunt)
- Add ref alt read depth #20 (martinghunt)
- Report read counts #19 (martinghunt)
- Refcheck max length #18 (martinghunt)
- Make sspace and gapfiller optional #17 (martinghunt)
- write bad checked ref seqs to file; fix genetic_code options #16 (martinghunt)
- Add summary task #15 (martinghunt)
- Check res genes #14 (martinghunt)
- Report percent identity and number bases assembled #13 (martinghunt)
- Use cd-hit-est #12 (martinghunt)
v0.2.0 (2015-02-20)
Merged pull requests:
- Version 0.1.2 -> 0.2.0 #11 (martinghunt)
- Use cdhit #10 (martinghunt)
v0.1.2 (2015-02-18)
Merged pull requests:
- Bux fixes velvet path #9 (martinghunt)
v0.1.1 (2015-02-18)
Merged pull requests:
- Update version to 0.1.1 #8 (martinghunt)
- Remove debugging sys.exit #7 (martinghunt)
v0.1.0 (2015-02-18)
Merged pull requests:
- Move usage info to wiki #6 (martinghunt)
- fix executables and paths #5 (martinghunt)
- Fix bugs finding paths of dependencies #4 (martinghunt)
- Use spades #3 (martinghunt)
- Add velvet to dependencies #2 (martinghunt)
v0.0.1 (2015-02-12)
Merged pull requests:
- Initial working version #1 (martinghunt)
* This Change Log was automatically generated by github_changelog_generator