CHANGELOG.md

Change Log

v2.13.4 (2019-03-15)

Full Changelog

Closed issues:

• Ariba run signal 28 #252
• NCBI database. #241

Merged pull requests:

• Allow increasing cd-hit-est memory allocation #255 #256 (kpepper)

v2.13.3 (2019-01-02)

Full Changelog

Merged pull requests:

• TB D94A fix #251 (martinghunt)

v2.13.2 (2018-12-21)

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Merged pull requests:

• Update tb panel #250 (martinghunt)
• Added changelog #248 (ssjunnebo)
• Update python min version #247 (ssjunnebo)

v2.13.1 (2018-11-16)

Full Changelog

Closed issues:

• resfinder line breaks problem #236

Merged pull requests:

• Include tb_data dir in release #244 (martinghunt)

v2.13.0 (2018-11-16)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Merged pull requests:

• fix card db path #213 (eppinglen)

v2.11.0-1 (2018-02-02)

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v2.11.0 (2018-02-02)

Full Changelog

Closed issues:

• micplot requires X window #176

Merged pull requests:

• Option to use Spades and multithreading for Bowtie2 and Spades #210 (andreyto)

v2.10.4 (2018-02-01)

Full Changelog

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)

Full Changelog

Closed issues:

• CARD downloads now bz2 #200

Merged pull requests:

• Mlst hetmin bug #204 (martinghunt)

v2.10.2 (2017-11-08)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Closed issues:

• pubmlstget does not work with docker #180
• getref broken on CARD v1.1.8 #178

Merged pull requests:

• Reviewer issues #182 (martinghunt)
• Task expandflag #181 (martinghunt)

v2.9.4 (2017-05-24)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Closed issues:

• Curious output #172
• How to input several fastq files for pooled assembly? #171

Merged pull requests:

• Bowtie2.3.1 #174 (martinghunt)

v2.9.1 (2017-04-07)

Full Changelog

Closed issues:

• Failing to build wheel #168
• add VirulenceFinder #165

Merged pull requests:

• Summary yes mutli het key error #173 (martinghunt)

v2.9.0 (2017-03-31)

Full Changelog

Closed issues:

• Ecoli no 1 profile warning #163
• Failed building wheel for ariba #161
• getref CARD #160

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)

Full Changelog

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)

Full Changelog

Merged pull requests:

• Require pymummer 0.10.2 #158 (martinghunt)

v2.7.1 (2017-01-27)

Full Changelog

Merged pull requests:

• Newick rooting bug #156 (martinghunt)
• Check BeautifulSoup version number #154 (martinghunt)

v2.7.0 (2017-01-17)

Full Changelog

Merged pull requests:

• Add megares #153 (martinghunt)

v2.6.1 (2016-12-21)

Full Changelog

Merged pull requests:

• Ignore additional columns in MLST profiles #152 (andrewjpage)

v2.6.0 (2016-12-20)

Full Changelog

Merged pull requests:

• Pubmlst #151 (martinghunt)

v2.5.1 (2016-12-05)

Full Changelog

Merged pull requests:

• Use flank length to choose best assembly #150 (martinghunt)

v2.5.0 (2016-11-18)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Merged pull requests:

• Bcftools ploidy #133 (martinghunt)

v2.2.4 (2016-08-23)

Full Changelog

Merged pull requests:

• Reportfilter bug #132 (martinghunt)

v2.2.3 (2016-08-22)

Full Changelog

Merged pull requests:

• bug fix summary when no samtools alt #131 (martinghunt)

v2.2.2 (2016-08-22)

Full Changelog

Merged pull requests:

• Contig renaming #130 (martinghunt)

v2.2.1 (2016-08-18)

Full Changelog

Merged pull requests:

• Aln2meta fix #129 (martinghunt)

v2.2.0 (2016-08-18)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Merged pull requests:

• Spades use untrusted-contigs #31 (martinghunt)

v0.4.0 (2015-06-10)

Full Changelog

Merged pull requests:

• Flag hit both strands #30 (martinghunt)
• Make cdhit optional #29 (martinghunt)

v0.3.2 (2015-05-12)

Full Changelog

Merged pull requests:

• Bug when samtools zero depth #28 (martinghunt)

v0.3.1 (2015-04-20)

Full Changelog

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)

Full Changelog

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)

Full Changelog

Merged pull requests:

• Version 0.1.2 -> 0.2.0 #11 (martinghunt)
• Use cdhit #10 (martinghunt)

v0.1.2 (2015-02-18)

Full Changelog

Merged pull requests:

• Bux fixes velvet path #9 (martinghunt)

v0.1.1 (2015-02-18)

Full Changelog

Merged pull requests:

• Update version to 0.1.1 #8 (martinghunt)
• Remove debugging sys.exit #7 (martinghunt)

v0.1.0 (2015-02-18)

Full Changelog

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