Fixed bugs:
- Infinite recursion in clean.py ? #123
Closed issues:
- how to use circlator on computer without internet access #108
Merged pull requests:
- fix readme and add to codecov #141 (ssjunnebo)
- Include Docker #137 (ssjunnebo)
- edit Dockerfile #136 (ssjunnebo)
- add Dockerfile #135 (ssjunnebo)
v1.5.5 (2018-01-31)
Closed issues:
- nucmer version detected by "circlator progcheck" but not "circlator all" #122
- Canu version is not being detected properly #113
Merged pull requests:
v1.5.4 (2018-01-31)
Closed issues:
- Problems running progcheck, error with installation? #124
Merged pull requests:
- Add tests for external version string checking #125 (andrewjpage)
v1.5.3 (2017-11-09)
Closed issues:
- Clarification regarding nanopore data #119
- nucmer version isn't detected correctly #117
- Error when running circlator: can't find canu version #111
- progcheck: found nucmer but couldn't get version #110
- Installation problem: command not found after pip3 install circlator #109
- memory usage #106
- Recompile with -fPIC error git / pip3 installs #103
- fixstart with user supplied gene sequences does not work #93
Merged pull requests:
- version bump #120 (ssjunnebo)
- fixes #110, #117 #118 (spock)
- circlator version #112 (ssjunnebo)
- update AUTHORS and LICENSE #94 (ssjunnebo)
v1.5.1 (2017-04-21)
Closed issues:
- Circlator with short reads? #88
Merged pull requests:
- Canu1.5 #89 (martinghunt)
v1.5.0 (2017-04-03)
Closed issues:
- version of SPAdes ? #85
- It looks like circlator keeps a common k-mer at the ends of a contig after changing start position. What for? #82
- Error running circlator with option --assemble_not_only_assembler #80
Merged pull requests:
- Add canu #87 (martinghunt)
- Included option --CanuCorrectedErrorRate to allow user to modify opti… #86 (NicolaDM)
- Splitting reads for small contigs when using Canu #84 (NicolaDM)
- Adding the option to use Canu instead of SPAdes #83 (NicolaDM)
v1.4.1 (2017-01-24)
Closed issues:
- Circularization of BAC contigs #79
- failure to circularise: cannot use this pair because longer match was found #75
- samtools command error #66
Merged pull requests:
- Fix assemble not only assembler #81 (martinghunt)
v1.4.0 (2016-10-17)
Closed issues:
Merged pull requests:
- Fixstart expose mincluster opt #77 (martinghunt)
v1.3.1 (2016-09-27)
Closed issues:
- SPAdes 3.7.1 recommendation #72
- Spades could not be detected #68
- fixstart fails if spaces in sequence names #64
Merged pull requests:
- Update dnaa #74 (martinghunt)
v1.3.0 (2016-08-12)
Closed issues:
- Spades version detection error #67
- minimus2 using hard-coded /usr/local/bin/show-coords #65
- Temporary folders not cleaned up when process killed #58
- Add --verbose to the other subcommands #57
- Spades version detection bit wonky? #56
- circlator fails and still creates the final output file 06.fixstart.fasta #55
- Error running circlator 0.14.0 to reproduce results from published article #54
Merged pull requests:
- Add --debug option to progcheck #71 (martinghunt)
- Spades python2 issues #70 (martinghunt)
- Refactor fixstart #69 (martinghunt)
v1.2.1 (2016-04-19)
Closed issues:
Merged pull requests:
- Bug fix running version task #63 (martinghunt)
- Version bump 1.2.1 #62 (martinghunt)
- Summarise circularizations #61 (martinghunt)
- Version reporting improvements #60 (martinghunt)
- add verbose option #59 (martinghunt)
v1.2.0 (2016-03-09)
Merged pull requests:
- Expose spades careful only assemble #53 (martinghunt)
v1.1.5 (2016-03-09)
Merged pull requests:
- Mapping tests #50 (martinghunt)
- support for samtools > 1.2 #49 (gedankenstuecke)
v1.1.4 (2016-02-19)
Closed issues:
- too many values to unpack error on merge command #44
Merged pull requests:
- Nucmer simplify true #47 (martinghunt)
- Make usage clearer #46 (martinghunt)
v1.1.3 (2016-01-25)
Closed issues:
- contig.fastg went missing because of SPAdes 3.6.1 output changes #39
Merged pull requests:
- Bug running merge (issue 44) #45 (martinghunt)
v1.1.2 (2015-11-30)
Merged pull requests:
- Spades 3.6.2 #43 (martinghunt)
v1.1.1 (2015-10-30)
Merged pull requests:
- Spades 3.6.1 #42 (martinghunt)
v1.1.0 (2015-10-20)
Closed issues:
- Numpy for python3 #30
Merged pull requests:
- More logging; better spades assembly; update dependencies #41 (martinghunt)
- Spades try all kmers #40 (martinghunt)
v1.0.2 (2015-09-03)
Closed issues:
- circlator progcheck report PATH of binary? #36
Merged pull requests:
- Dnaa filtering #38 (martinghunt)
v1.0.1 (2015-09-01)
Merged pull requests:
- Progcheck report full paths #37 (martinghunt)
v1.0.0 (2015-08-24)
Merged pull requests:
- Generalise get_dnaa; write versions etc info file #35 (martinghunt)
v0.16.1 (2015-08-20)
Merged pull requests:
- Require fastaq 3.6.1; version bump #34 (martinghunt)
- Add travis #32 (martinghunt)
- Added AUTHORS with mh12 as author #29 (aslett1)
v0.16.0 (2015-08-12)
Merged pull requests:
- New task progcheck #28 (martinghunt)
- New task get_dnaa; update dnaA fasta file #27 (martinghunt)
v0.15.1 (2015-07-31)
Merged pull requests:
- bug fix fixstart --ignore option #26 (martinghunt)
v0.15.0 (2015-07-29)
Merged pull requests:
- sanity check input; contig filtering #25 (martinghunt)
- Remove mention of bacteria #24 (martinghunt)
- help exits without error #23 (andrewjpage)
v0.14.2 (2015-07-10)
Merged pull requests:
- add homebrew command #22 (andrewjpage)
- Fix a few typos #21 (martinghunt)
v0.14.1 (2015-06-24)
Merged pull requests:
- do not ignore log files #20 (martinghunt)
- Clean refactor #19 (martinghunt)
v0.14.0 (2015-06-04)
Closed issues:
- Install failed - bio-assembly-refinement/setup.py", line 6, #13
Merged pull requests:
- Expose spades kmer #18 (martinghunt)
v0.13.2 (2015-06-02)
Merged pull requests:
- Use second best hits #17 (martinghunt)
v0.13.1 (2015-05-29)
Merged pull requests:
- Minimus2 error typos #16 (martinghunt)
v0.13.0 (2015-05-28)
Merged pull requests:
- Use nucmer diagdiff #15 (martinghunt)
- Add wrapper for minimus2 pipeline #14 (martinghunt)
- Update readme #12 (martinghunt)
v0.12.1 (2015-05-21)
Merged pull requests:
- Fix usage typos #11 (martinghunt)
v0.12.0 (2015-05-20)
Merged pull requests:
- Write final FASTG file #10 (martinghunt)
- Tidy output and usage #9 (martinghunt)
- add circularised to column to merge log #8 (martinghunt)
- trim reads kept from contig ends #7 (martinghunt)
- Use spades graph #6 (martinghunt)
- Do not break reads #5 (martinghunt)
v0.2.0 (2015-04-16)
Merged pull requests:
- make default merge less permissive #4 (martinghunt)
- Add option to not fix start of some contigs #3 (martinghunt)
- Include default genes fa #2 (martinghunt)
- Initial version #1 (martinghunt)