Fixed bugs:
- Run fails if Aragorn predicts unreliable anticodons #61
Closed issues:
- sudo #57
Merged pull requests:
- Final (?) documentation rewrite #89 (trstickland)
- Doc rewrite #88 (trstickland)
- travis CI now pulls rather than builds the docker image #86 (trstickland)
- travis build fixed #83 (trstickland)
- snap wasn't in PATH; symlink from /usr/local/bin #82 (trstickland)
- Docker build fail #81 (trstickland)
- update readme format #79 (ssjunnebo)
- add AUTHORS file #78 (ssjunnebo)
- add systematic ID #75 (satta)
- add multiple transcript qualifiers #73 (satta)
- ensure that reports step always finishes with required files #72 (satta)
- ignore nonzero exit codes from speck #71 (satta)
- Repo cleanup #70 (satta)
- Stability and robustness fixes #69 (satta)
- Robustness improvements #67 (satta)
- major improvements to EMBL converter #66 (satta)
- separate genes and pseudogenes in stats generation #65 (satta)
- use correct package name in testing #64 (satta)
- EMBL export improvements #63 (satta)
- Bug fixes, cleanups and robustness improvements #62 (satta)
- Include UTRs in EMBL conversion #60 (satta)
- Channel
hintschannel is never used. #59 (pditommaso) - always truncate inputs before sanitizing #58 (satta)
v1.0.1 (2016-04-05)
Implemented enhancements:
Fixed bugs:
- Proactive sanitization of input headers with special characters #49
Merged pull requests:
- Address problems with EMBL output #56 (satta)
- small fixes #54 (satta)
- various improvements #53 (satta)
- use new version of libgsl package #50 (satta)
v1.0.0 (2016-01-28)
Implemented enhancements:
- Allow optional alphanumeric random locus tags #45
Fixed bugs:
- Missing SVG Perl module #1
Merged pull requests:
- ENA validation and ID assignment #46 (satta)
- 'Finish line' fixes towards ENA validity #43 (satta)
- allow pipeline to complete when no genes are annotated at all #42 (satta)
- Make sure Docker Hub builds working images #41 (satta)
- Stability improvements #40 (satta)
- fix Circos drawing #39 (satta)
- use whole genome as RATT input, not just chromosomes #38 (satta)
- use new Docker hub container #37 (satta)
- pseudogene and chromosome handling #36 (satta)
- skip Pfam hits with invalid converted ranges #35 (satta)
- Latest work #34 (satta)
- small fixes #33 (satta)
- Robustness improvement #32 (satta)
- Latest work #31 (satta)
- do not treat lowercase input sequences as repeat masked in LAST #30 (satta)
- AGP output and RATT integration #29 (satta)
- fixes and improvements #28 (satta)
- fixes and improvements #27 (satta)
- fixes and improvements #26 (satta)
- fixes and improvements #25 (satta)
- some polishing of pipeline output and postprocessing #24 (satta)
- make AGP splitting seqid comparisons more stringent #23 (satta)
- only keep metadata in references.json #22 (satta)
- integrate ab initio models into reference directory #21 (satta)
- update reference examples #20 (satta)
- make sure to fix ownership on Docker #19 (satta)
- do not fail on rm #18 (satta)
- clean up after RATT #17 (satta)
- add features and cleanup #16 (satta)
- allow transcript evidence #15 (satta)
- small fixes/improvements #14 (satta)
- make weight definition for integration step user configurable #13 (satta)
- some improvements #12 (satta)
- some work on stability and variety #11 (satta)
- simplify and improve EMBL export for RATT #10 (satta)
- fix Circos bin drawing #9 (satta)
- do not treat reference chromosome 'numbers' as numbers #8 (satta)
- add tantan, make PTU smoothing optional #7 (satta)
- use correct Travis build badge #6 (satta)
- use $baseDir consistently #5 (satta)
- Manual merge of pull request #2 #4 (satta)
- Use into operator with closure syntax #3 (pditommaso)