Merged pull requests:
- Update readme #87 (ssjunnebo)
- Point install instruction to webpage #84 (ssjunnebo)
- update README and add to codecov #83 (ssjunnebo)
- Docker instructions #82 (ssjunnebo)
- Set up Docker #81 (ssjunnebo)
v1.0.9-2 (2018-02-02)
v1.0.9-1 (2018-02-02)
Closed issues:
- iva version check of external programs fails #78
v1.0.9 (2018-01-25)
Closed issues:
- kmc std::bad_alloc #77
- samtools sort command fails for samtools 1.3.1 #75
- iva test failing with samtools1.4 #74
- IVA sensitivity threshold #72
- multithreading smalt error #71
Merged pull requests:
- Prog versions #79 (andrewjpage)
- test more samtools versions and pythons #76 (andrewjpage)
- update LICENSE and AUTHORS #73 (ssjunnebo)
v1.0.8 (2017-01-12)
Merged pull requests:
- Embl no cds fix #70 (martinghunt)
- upstreaming some patches #69 (satta)
v1.0.7 (2016-09-06)
Merged pull requests:
- Pysam 0.9.1.x #68 (martinghunt)
v1.0.6 (2016-05-12)
Closed issues:
- samtools errors caused by mapping.py #59
Merged pull requests:
- Flag reference opt as experimental #67 (martinghunt)
- Add travis files #66 (martinghunt)
v1.0.5 (2016-05-05)
Closed issues:
- Support samtools 1.3 #57
Merged pull requests:
- Version bump 1.0.5 #65 (martinghunt)
- fix spelling #64 (satta)
- add copyright notices #62 (satta)
- make IVA compatible with new 'samtools sort' syntax #61 (satta)
v1.0.4 (2016-04-18)
Closed issues:
- IVA: error: unrecognized arguments: path_to_output_directory #56
- thread option not passed to kmc #54
Merged pull requests:
- pysam 0.9.0 #58 (martinghunt)
v1.0.3 (2016-01-25)
Closed issues:
- support an explicit output argument #53
Merged pull requests:
- Kmc threads #55 (martinghunt)
v1.0.2 (2015-10-28)
Merged pull requests:
- Check samtools version #52 (martinghunt)
v1.0.1 (2015-10-16)
Merged pull requests:
- Use pyfastaq 3.10.0 #51 (martinghunt)
- import stat required to stop --add_to_ref dying #50 (martinghunt)
v1.0.0 (2015-07-15)
Merged pull requests:
- Make tests pass from last merge #49 (martinghunt)
- No strand bias trim #48 (martinghunt)
v0.11.7 (2015-07-09)
Merged pull requests:
- version bump, tweak setup.py #47 (martinghunt)
- Die nicely if input reads bad, or when no contigs made #46 (martinghunt)
v0.11.6 (2015-05-12)
Merged pull requests:
- Bug reusing bad kmers #45 (martinghunt)
- Bug fix - min contig length now implemented properly #44 (martinghunt)
v0.11.5 (2015-03-27)
Merged pull requests:
- Increment version #43 (martinghunt)
- Qc input checks #42 (martinghunt)
- Fix gage bugs #41 (martinghunt)
v0.11.4 (2015-02-24)
Merged pull requests:
- No really, make all ratt script executable #40 (martinghunt)
v0.11.3 (2015-02-24)
Merged pull requests:
- bug fix running ratt scripts #39 (martinghunt)
v0.11.2 (2015-02-05)
Merged pull requests:
- Remove info that is on the gh-pages site #38 (martinghunt)
- Change to pyfastaq #37 (martinghunt)
v0.11.0 (2015-01-29)
Merged pull requests:
- Change default extension parameters, bump to version 0.11.0 #36 (martinghunt)
v0.10.3 (2015-01-14)
Merged pull requests:
- Allow gage to fail as long as we got the stats; v0.10.3 #35 (martinghunt)
v0.10.2 (2015-01-07)
Merged pull requests:
- version 0.10.2 #34 (martinghunt)
v0.10.1 (2014-12-05)
Merged pull requests:
- Bug fixes: string decoding and qc write contigs file #33 (martinghunt)
- Link to the pathogens VM #32 (martinghunt)
v0.10.0 (2014-11-06)
Merged pull requests:
- Improve read trimming; version 0.10.0 #31 (martinghunt)
v0.9.0 (2014-10-02)
1.5.0 (2014-10-02)
Merged pull requests:
- version 0.9.0 #30 (martinghunt)
- write contigs that do not match reference #29 (martinghunt)
- Add ubuntu installation wiki link #28 (martinghunt)
- Contig trim #27 (martinghunt)
v0.8.0 (2014-09-11)
Merged pull requests:
- Pcr primer #26 (martinghunt)
- Added AUTHORS file #25 (aslett1)
v0.7.2 (2014-08-27)
v0.7.1 (2014-08-05)
v0.7.0 (2014-08-01)
v0.6.0 (2014-07-25)
v0.5.1 (2014-06-17)
v0.5.0 (2014-06-12)
Merged pull requests:
- Version 0.5.0 #24 (martinghunt)
- Qc cleanup #23 (martinghunt)
v0.4.0 (2014-06-11)
Merged pull requests:
- Change default QC percent identities to 80 #22 (martinghunt)
- Die gracefully if cannot find reference #21 (martinghunt)
- Add test embl files #20 (martinghunt)
- merge tidy_up_for_v0.4.0 #19 (martinghunt)
- merge add_custom_ref_to_db #18 (martinghunt)
- Tidy up checking external programs OK #17 (martinghunt)
- Add citation for adapter sequences #16 (martinghunt)
- Don't write final ORFs file #15 (martinghunt)
- Delete gage-validation.tar.gz #14 (martinghunt)
- Keep gage and ratt code and adapters.fasta files when installing #13 (martinghunt)
- Add checks for external programs in qc scripts #12 (martinghunt)
- Run kraken on reads sampled uniformly across assembly #11 (martinghunt)
- Add QC info and citations #10 (martinghunt)
- Use same function for all syscalls, so stdout/err only printed when some... #9 (martinghunt)
- Add default adapters file #8 (martinghunt)
- Add gage code, make gage defaults more permissive #7 (martinghunt)
- Catch mpileup lines with no read bases #6 (martinghunt)
- Assemble speed increase by using reads more intelligently #5 (martinghunt)
- Don't initialize sets, dicts etc in function declarations #4 (martinghunt)
v0.3.0 (2014-05-02)
Merged pull requests:
- Fix missing genome parts #3 (martinghunt)
v0.2.4 (2014-04-30)
Merged pull requests:
- Fix max_insert typo #2 (martinghunt)
- Initial add of files and update readme #1 (martinghunt)