# Change Log

## [v18.2.0](https://github.com/sanger-pathogens/artemis/tree/v18.2.0) (2022-03-16)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.1.0...v18.2.0)

## [v18.1.0](https://github.com/sanger-pathogens/artemis/tree/v18.1.0) (2019-12-04)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.3...v18.1.0)

## [v18.0.3](https://github.com/sanger-pathogens/artemis/tree/v18.0.3) (2019-08-07)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.2...v18.0.3)

**Closed issues:**

- Artemis vs. Java [\#293](https://github.com/sanger-pathogens/Artemis/issues/293)
- For windows Error: A JNI error has occurred, please check your installation and try again [\#292](https://github.com/sanger-pathogens/Artemis/issues/292)
- Supported JDKs/JREs [\#290](https://github.com/sanger-pathogens/Artemis/issues/290)
- Cannot install Java 9 on MacOSX [\#288](https://github.com/sanger-pathogens/Artemis/issues/288)
- unrecognized option [\#287](https://github.com/sanger-pathogens/Artemis/issues/287)
- no .jar files in Artemis download [\#285](https://github.com/sanger-pathogens/Artemis/issues/285)
- Problem installing via conda [\#284](https://github.com/sanger-pathogens/Artemis/issues/284)
- I am trying to open Artemis in windows 10 pro.  The screen is not opening [\#283](https://github.com/sanger-pathogens/Artemis/issues/283)

**Merged pull requests:**

- Add a docker file, build and documentation updates. Fix for issue 293. [\#294](https://github.com/sanger-pathogens/Artemis/pull/294) ([kpepper](https://github.com/kpepper))
- RT ticket 621414 - addition of source field to Gene Builder GO Term panel [\#289](https://github.com/sanger-pathogens/Artemis/pull/289) ([kpepper](https://github.com/kpepper))
- Documentation update for bioconda installs [\#286](https://github.com/sanger-pathogens/Artemis/pull/286) ([kpepper](https://github.com/kpepper))
- Add Bioconda badge [\#282](https://github.com/sanger-pathogens/Artemis/pull/282) ([kpepper](https://github.com/kpepper))
- Added additional course link [\#281](https://github.com/sanger-pathogens/Artemis/pull/281) ([kpepper](https://github.com/kpepper))
- Added documentation and courses sections [\#280](https://github.com/sanger-pathogens/Artemis/pull/280) ([kpepper](https://github.com/kpepper))
- Documentation updates [\#279](https://github.com/sanger-pathogens/Artemis/pull/279) ([kpepper](https://github.com/kpepper))

## [v18.0.2](https://github.com/sanger-pathogens/artemis/tree/v18.0.2) (2019-02-06)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.1...v18.0.2)

**Merged pull requests:**

- RT Ticket 648115 blast issue [\#278](https://github.com/sanger-pathogens/Artemis/pull/278) ([kpepper](https://github.com/kpepper))
- Fix for RT ticket 649125 [\#277](https://github.com/sanger-pathogens/Artemis/pull/277) ([kpepper](https://github.com/kpepper))
- Added information on installation via Bioconda [\#276](https://github.com/sanger-pathogens/Artemis/pull/276) ([kpepper](https://github.com/kpepper))
- Updated Artemis release number to v18.0.1 [\#275](https://github.com/sanger-pathogens/Artemis/pull/275) ([kpepper](https://github.com/kpepper))

## [v18.0.1](https://github.com/sanger-pathogens/artemis/tree/v18.0.1) (2019-01-22)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.0...v18.0.1)

**Merged pull requests:**

- Artemis Release v18.0.1 draft changes [\#274](https://github.com/sanger-pathogens/Artemis/pull/274) ([kpepper](https://github.com/kpepper))
- Autogenerate CHANGELOG.md [\#273](https://github.com/sanger-pathogens/Artemis/pull/273) ([ssjunnebo](https://github.com/ssjunnebo))
- Added section on security warnings for Macs [\#272](https://github.com/sanger-pathogens/Artemis/pull/272) ([kpepper](https://github.com/kpepper))
- Artemis v18.0.0 Documentation Changes [\#271](https://github.com/sanger-pathogens/Artemis/pull/271) ([kpepper](https://github.com/kpepper))

## [v18.0.0](https://github.com/sanger-pathogens/artemis/tree/v18.0.0) (2019-01-07)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.0-RC1...v18.0.0)

**Merged pull requests:**

- Merge build 18.0.0 changes to master [\#270](https://github.com/sanger-pathogens/Artemis/pull/270) ([kpepper](https://github.com/kpepper))
- Prep for Release 18.0.0 [\#269](https://github.com/sanger-pathogens/Artemis/pull/269) ([kpepper](https://github.com/kpepper))

## [v18.0.0-RC1](https://github.com/sanger-pathogens/artemis/tree/v18.0.0-RC1) (2018-12-13)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v17.0.1...v18.0.0-RC1)

**Closed issues:**

- "This version of Mac OS X does not support the Apple EAWT." [\#267](https://github.com/sanger-pathogens/Artemis/issues/267)
- Artemis on server [\#264](https://github.com/sanger-pathogens/Artemis/issues/264)
- Can not use Artemis [\#263](https://github.com/sanger-pathogens/Artemis/issues/263)
- Run fails: Could not find or load main class uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions ``` [\#261](https://github.com/sanger-pathogens/Artemis/issues/261)
- What's the entry point for Bamview in artemis.jar ? [\#240](https://github.com/sanger-pathogens/Artemis/issues/240)
- artemis\_compiled\_v17.0.1.tar.gz has all MacOS resource forks in it [\#239](https://github.com/sanger-pathogens/Artemis/issues/239)
- Feature Request: recognize and open multi-genbanks in multiple seperate windows [\#236](https://github.com/sanger-pathogens/Artemis/issues/236)

**Merged pull requests:**

- Committed Artemis and ACT word master docs from which HTML and PDF ma… [\#268](https://github.com/sanger-pathogens/Artemis/pull/268) ([kpepper](https://github.com/kpepper))
- Added the Chado folder [\#266](https://github.com/sanger-pathogens/Artemis/pull/266) ([kpepper](https://github.com/kpepper))
- Add Artemis and ACT html/pdf manuals to gh-pages branch [\#265](https://github.com/sanger-pathogens/Artemis/pull/265) ([kpepper](https://github.com/kpepper))
- Fixed GitHub issue 261 - escaped line feed left in manifest when buil… [\#262](https://github.com/sanger-pathogens/Artemis/pull/262) ([kpepper](https://github.com/kpepper))
- Fix for RT issue 624271 - bam data caching issue [\#260](https://github.com/sanger-pathogens/Artemis/pull/260) ([kpepper](https://github.com/kpepper))
- Various updates to github pages, inc removal of sourceforge references. [\#259](https://github.com/sanger-pathogens/Artemis/pull/259) ([kpepper](https://github.com/kpepper))
- 589110 readme [\#258](https://github.com/sanger-pathogens/Artemis/pull/258) ([ssjunnebo](https://github.com/ssjunnebo))
- Remove windows download note [\#257](https://github.com/sanger-pathogens/Artemis/pull/257) ([ssjunnebo](https://github.com/ssjunnebo))
- update downloads [\#256](https://github.com/sanger-pathogens/Artemis/pull/256) ([ssjunnebo](https://github.com/ssjunnebo))
- Show favicon on all pages [\#255](https://github.com/sanger-pathogens/Artemis/pull/255) ([ssjunnebo](https://github.com/ssjunnebo))
- remove downloads from artemis page [\#254](https://github.com/sanger-pathogens/Artemis/pull/254) ([ssjunnebo](https://github.com/ssjunnebo))
- add favicon [\#253](https://github.com/sanger-pathogens/Artemis/pull/253) ([ssjunnebo](https://github.com/ssjunnebo))
- update ftp downloads [\#252](https://github.com/sanger-pathogens/Artemis/pull/252) ([ssjunnebo](https://github.com/ssjunnebo))
- fix links [\#251](https://github.com/sanger-pathogens/Artemis/pull/251) ([ssjunnebo](https://github.com/ssjunnebo))
- change header name [\#250](https://github.com/sanger-pathogens/Artemis/pull/250) ([ssjunnebo](https://github.com/ssjunnebo))
- update Artemis page [\#249](https://github.com/sanger-pathogens/Artemis/pull/249) ([ssjunnebo](https://github.com/ssjunnebo))
- Update layout [\#248](https://github.com/sanger-pathogens/Artemis/pull/248) ([ssjunnebo](https://github.com/ssjunnebo))
- Transfer content from Sanger web pages [\#247](https://github.com/sanger-pathogens/Artemis/pull/247) ([ssjunnebo](https://github.com/ssjunnebo))
- Change page header [\#246](https://github.com/sanger-pathogens/Artemis/pull/246) ([ssjunnebo](https://github.com/ssjunnebo))
- 574328 update readme [\#245](https://github.com/sanger-pathogens/Artemis/pull/245) ([ssjunnebo](https://github.com/ssjunnebo))
- include faq etc [\#244](https://github.com/sanger-pathogens/Artemis/pull/244) ([ssjunnebo](https://github.com/ssjunnebo))
- Added more content [\#243](https://github.com/sanger-pathogens/Artemis/pull/243) ([ssjunnebo](https://github.com/ssjunnebo))
- first draft of gh pages [\#242](https://github.com/sanger-pathogens/Artemis/pull/242) ([ssjunnebo](https://github.com/ssjunnebo))
- Set up github pages [\#241](https://github.com/sanger-pathogens/Artemis/pull/241) ([ssjunnebo](https://github.com/ssjunnebo))

## [v17.0.1](https://github.com/sanger-pathogens/artemis/tree/v17.0.1) (2018-03-09)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v17.0.0...v17.0.1)

**Merged pull requests:**

- small increase in splash height for ubuntu [\#238](https://github.com/sanger-pathogens/Artemis/pull/238) ([kpepper](https://github.com/kpepper))
- V17 patch branch [\#237](https://github.com/sanger-pathogens/Artemis/pull/237) ([kpepper](https://github.com/kpepper))
- Rebranded splash screen [\#235](https://github.com/sanger-pathogens/Artemis/pull/235) ([kpepper](https://github.com/kpepper))

## [v17.0.0](https://github.com/sanger-pathogens/artemis/tree/v17.0.0) (2018-02-12)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v16.0.17...v17.0.0)

**Closed issues:**

- reading features from entries in BED\(12\) format [\#232](https://github.com/sanger-pathogens/Artemis/issues/232)
- Artemis not opening files with brackets/space/altered name [\#229](https://github.com/sanger-pathogens/Artemis/issues/229)
- Why blast shows no response? [\#228](https://github.com/sanger-pathogens/Artemis/issues/228)
- java.lang.NullPointerException [\#227](https://github.com/sanger-pathogens/Artemis/issues/227)

**Merged pull requests:**

- Changed BamUtilsTest class to cope with connect exception. [\#234](https://github.com/sanger-pathogens/Artemis/pull/234) ([kpepper](https://github.com/kpepper))
- Artemis unit testing v17.0.0 branch merge [\#233](https://github.com/sanger-pathogens/Artemis/pull/233) ([kpepper](https://github.com/kpepper))
- update scratch108 to scratch118 - v16.0.18 [\#230](https://github.com/sanger-pathogens/Artemis/pull/230) ([vaofford](https://github.com/vaofford))

## [v16.0.17](https://github.com/sanger-pathogens/artemis/tree/v16.0.17) (2016-11-23)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v16.0.0...v16.0.17)

**Closed issues:**

- .embl file not working in Artemis [\#222](https://github.com/sanger-pathogens/Artemis/issues/222)

**Merged pull requests:**

- Updated NCBI blast URL to https [\#226](https://github.com/sanger-pathogens/Artemis/pull/226) ([aslett1](https://github.com/aslett1))
- version bump [\#225](https://github.com/sanger-pathogens/Artemis/pull/225) ([satta](https://github.com/satta))
- add TCDB as database [\#221](https://github.com/sanger-pathogens/Artemis/pull/221) ([satta](https://github.com/satta))
- fix method name clash for List.sort\(\) in Java 8 [\#220](https://github.com/sanger-pathogens/Artemis/pull/220) ([satta](https://github.com/satta))
- switch to older EMBOSS version [\#219](https://github.com/sanger-pathogens/Artemis/pull/219) ([satta](https://github.com/satta))
- override abstract method close\(\) in CRAMReferenceSequenceFile [\#218](https://github.com/sanger-pathogens/Artemis/pull/218) ([0xaf1f](https://github.com/0xaf1f))
- Added Kim Rutherford [\#217](https://github.com/sanger-pathogens/Artemis/pull/217) ([aslett1](https://github.com/aslett1))
- Add TravisCI Support, change README to markdown [\#215](https://github.com/sanger-pathogens/Artemis/pull/215) ([bewt85](https://github.com/bewt85))
- actually clone the history attribute [\#214](https://github.com/sanger-pathogens/Artemis/pull/214) ([satta](https://github.com/satta))
- add support for eupathdb\_uc user comment attributes [\#213](https://github.com/sanger-pathogens/Artemis/pull/213) ([satta](https://github.com/satta))
- add new 'alias' qualifier [\#212](https://github.com/sanger-pathogens/Artemis/pull/212) ([satta](https://github.com/satta))
- Added uORF, sORF and tnaORF as extra keys [\#211](https://github.com/sanger-pathogens/Artemis/pull/211) ([fatimasilva](https://github.com/fatimasilva))
- extend escaping in qualifier values [\#210](https://github.com/sanger-pathogens/Artemis/pull/210) ([satta](https://github.com/satta))
- Added AUTHORS file [\#209](https://github.com/sanger-pathogens/Artemis/pull/209) ([aslett1](https://github.com/aslett1))
- Added LICENSE [\#208](https://github.com/sanger-pathogens/Artemis/pull/208) ([aslett1](https://github.com/aslett1))
- simplify regex for user comment scraping [\#207](https://github.com/sanger-pathogens/Artemis/pull/207) ([satta](https://github.com/satta))
- add tritryp\_uc attribute to GFF3 export [\#206](https://github.com/sanger-pathogens/Artemis/pull/206) ([satta](https://github.com/satta))
- do not always strip 'term=' from product [\#205](https://github.com/sanger-pathogens/Artemis/pull/205) ([satta](https://github.com/satta))
- add user\_data\_min and user\_data\_max flags [\#204](https://github.com/sanger-pathogens/Artemis/pull/204) ([tcarver](https://github.com/tcarver))
- allow user plots scaling to be controlled with user\_scaling\_on [\#203](https://github.com/sanger-pathogens/Artemis/pull/203) ([tcarver](https://github.com/tcarver))
- misc [\#202](https://github.com/sanger-pathogens/Artemis/pull/202) ([tcarver](https://github.com/tcarver))
- misc [\#201](https://github.com/sanger-pathogens/Artemis/pull/201) ([tcarver](https://github.com/tcarver))
- misc [\#200](https://github.com/sanger-pathogens/Artemis/pull/200) ([tcarver](https://github.com/tcarver))
- remove quotes [\#199](https://github.com/sanger-pathogens/Artemis/pull/199) ([tcarver](https://github.com/tcarver))
- misc [\#198](https://github.com/sanger-pathogens/Artemis/pull/198) ([tcarver](https://github.com/tcarver))
- misc [\#197](https://github.com/sanger-pathogens/Artemis/pull/197) ([tcarver](https://github.com/tcarver))
- misc [\#196](https://github.com/sanger-pathogens/Artemis/pull/196) ([tcarver](https://github.com/tcarver))
- misc [\#195](https://github.com/sanger-pathogens/Artemis/pull/195) ([tcarver](https://github.com/tcarver))
- fix for paired stack view when showing SNPs [\#194](https://github.com/sanger-pathogens/Artemis/pull/194) ([tcarver](https://github.com/tcarver))
- misc [\#193](https://github.com/sanger-pathogens/Artemis/pull/193) ([tcarver](https://github.com/tcarver))
- misc [\#191](https://github.com/sanger-pathogens/Artemis/pull/191) ([tcarver](https://github.com/tcarver))
- ignore codon\_start when writing out [\#189](https://github.com/sanger-pathogens/Artemis/pull/189) ([tcarver](https://github.com/tcarver))
- increase default threshold [\#188](https://github.com/sanger-pathogens/Artemis/pull/188) ([tcarver](https://github.com/tcarver))
- misc [\#187](https://github.com/sanger-pathogens/Artemis/pull/187) ([tcarver](https://github.com/tcarver))
- fix for writing GFF qualifiers and stripping out current= [\#186](https://github.com/sanger-pathogens/Artemis/pull/186) ([tcarver](https://github.com/tcarver))
- misc [\#185](https://github.com/sanger-pathogens/Artemis/pull/185) ([tcarver](https://github.com/tcarver))
- misc [\#184](https://github.com/sanger-pathogens/Artemis/pull/184) ([tcarver](https://github.com/tcarver))
- Sascha GFF export and GFF encode / decode changes [\#183](https://github.com/sanger-pathogens/Artemis/pull/183) ([tcarver](https://github.com/tcarver))
- misc [\#181](https://github.com/sanger-pathogens/Artemis/pull/181) ([tcarver](https://github.com/tcarver))
- use uniprot.org for protein links [\#180](https://github.com/sanger-pathogens/Artemis/pull/180) ([tcarver](https://github.com/tcarver))
- misc [\#179](https://github.com/sanger-pathogens/Artemis/pull/179) ([tcarver](https://github.com/tcarver))
- misc [\#178](https://github.com/sanger-pathogens/Artemis/pull/178) ([tcarver](https://github.com/tcarver))
- misc [\#177](https://github.com/sanger-pathogens/Artemis/pull/177) ([tcarver](https://github.com/tcarver))

## [v16.0.0](https://github.com/sanger-pathogens/artemis/tree/v16.0.0) (2014-01-14)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v15.0.0...v16.0.0)

**Merged pull requests:**

- misc [\#176](https://github.com/sanger-pathogens/Artemis/pull/176) ([tcarver](https://github.com/tcarver))
- allow to exclude attributes from GFF3 output [\#175](https://github.com/sanger-pathogens/Artemis/pull/175) ([satta](https://github.com/satta))
- do not output empty GFF3 attributes [\#174](https://github.com/sanger-pathogens/Artemis/pull/174) ([satta](https://github.com/satta))
- misc [\#173](https://github.com/sanger-pathogens/Artemis/pull/173) ([tcarver](https://github.com/tcarver))
- misc [\#172](https://github.com/sanger-pathogens/Artemis/pull/172) ([tcarver](https://github.com/tcarver))
- misc [\#171](https://github.com/sanger-pathogens/Artemis/pull/171) ([tcarver](https://github.com/tcarver))
- warn when overlaying a GFF with a sequence onto a sequence entry [\#170](https://github.com/sanger-pathogens/Artemis/pull/170) ([tcarver](https://github.com/tcarver))
- fix for ACT jnlp VM properties [\#169](https://github.com/sanger-pathogens/Artemis/pull/169) ([tcarver](https://github.com/tcarver))
- fix for ACT jnlp VM properties [\#168](https://github.com/sanger-pathogens/Artemis/pull/168) ([tcarver](https://github.com/tcarver))
- misc [\#167](https://github.com/sanger-pathogens/Artemis/pull/167) ([tcarver](https://github.com/tcarver))
- updates for test [\#166](https://github.com/sanger-pathogens/Artemis/pull/166) ([tcarver](https://github.com/tcarver))
- misc [\#165](https://github.com/sanger-pathogens/Artemis/pull/165) ([tcarver](https://github.com/tcarver))
- update [\#164](https://github.com/sanger-pathogens/Artemis/pull/164) ([tcarver](https://github.com/tcarver))
- misc [\#163](https://github.com/sanger-pathogens/Artemis/pull/163) ([tcarver](https://github.com/tcarver))
- misc [\#162](https://github.com/sanger-pathogens/Artemis/pull/162) ([tcarver](https://github.com/tcarver))
- misc [\#161](https://github.com/sanger-pathogens/Artemis/pull/161) ([tcarver](https://github.com/tcarver))
- misc [\#160](https://github.com/sanger-pathogens/Artemis/pull/160) ([tcarver](https://github.com/tcarver))
- misc [\#159](https://github.com/sanger-pathogens/Artemis/pull/159) ([tcarver](https://github.com/tcarver))
- misc [\#158](https://github.com/sanger-pathogens/Artemis/pull/158) ([tcarver](https://github.com/tcarver))
- misc [\#157](https://github.com/sanger-pathogens/Artemis/pull/157) ([tcarver](https://github.com/tcarver))
- misc [\#156](https://github.com/sanger-pathogens/Artemis/pull/156) ([tcarver](https://github.com/tcarver))
- bamview update [\#155](https://github.com/sanger-pathogens/Artemis/pull/155) ([tcarver](https://github.com/tcarver))
- update version [\#154](https://github.com/sanger-pathogens/Artemis/pull/154) ([tcarver](https://github.com/tcarver))
- misc [\#153](https://github.com/sanger-pathogens/Artemis/pull/153) ([tcarver](https://github.com/tcarver))
- misc [\#152](https://github.com/sanger-pathogens/Artemis/pull/152) ([tcarver](https://github.com/tcarver))
- mics [\#151](https://github.com/sanger-pathogens/Artemis/pull/151) ([tcarver](https://github.com/tcarver))
- rename [\#150](https://github.com/sanger-pathogens/Artemis/pull/150) ([tcarver](https://github.com/tcarver))
- misc [\#149](https://github.com/sanger-pathogens/Artemis/pull/149) ([tcarver](https://github.com/tcarver))
- misc [\#148](https://github.com/sanger-pathogens/Artemis/pull/148) ([tcarver](https://github.com/tcarver))
- misc [\#147](https://github.com/sanger-pathogens/Artemis/pull/147) ([tcarver](https://github.com/tcarver))
- misc [\#145](https://github.com/sanger-pathogens/Artemis/pull/145) ([tcarver](https://github.com/tcarver))
- misc [\#144](https://github.com/sanger-pathogens/Artemis/pull/144) ([tcarver](https://github.com/tcarver))
- fix for validate button on linux  [\#143](https://github.com/sanger-pathogens/Artemis/pull/143) ([tcarver](https://github.com/tcarver))
- misc [\#142](https://github.com/sanger-pathogens/Artemis/pull/142) ([tcarver](https://github.com/tcarver))
- misc [\#141](https://github.com/sanger-pathogens/Artemis/pull/141) ([tcarver](https://github.com/tcarver))
- misc [\#140](https://github.com/sanger-pathogens/Artemis/pull/140) ([tcarver](https://github.com/tcarver))
- update version [\#139](https://github.com/sanger-pathogens/Artemis/pull/139) ([tcarver](https://github.com/tcarver))
- misc [\#138](https://github.com/sanger-pathogens/Artemis/pull/138) ([tcarver](https://github.com/tcarver))
- misc [\#137](https://github.com/sanger-pathogens/Artemis/pull/137) ([tcarver](https://github.com/tcarver))
- misc [\#136](https://github.com/sanger-pathogens/Artemis/pull/136) ([tcarver](https://github.com/tcarver))
- update version [\#135](https://github.com/sanger-pathogens/Artemis/pull/135) ([tcarver](https://github.com/tcarver))
- misc [\#134](https://github.com/sanger-pathogens/Artemis/pull/134) ([tcarver](https://github.com/tcarver))
- rnaseq strand specific option [\#133](https://github.com/sanger-pathogens/Artemis/pull/133) ([tcarver](https://github.com/tcarver))
- misc [\#132](https://github.com/sanger-pathogens/Artemis/pull/132) ([tcarver](https://github.com/tcarver))
- misc [\#131](https://github.com/sanger-pathogens/Artemis/pull/131) ([tcarver](https://github.com/tcarver))
- misc [\#130](https://github.com/sanger-pathogens/Artemis/pull/130) ([tcarver](https://github.com/tcarver))
- misc [\#129](https://github.com/sanger-pathogens/Artemis/pull/129) ([tcarver](https://github.com/tcarver))

## [v15.0.0](https://github.com/sanger-pathogens/artemis/tree/v15.0.0) (2013-02-15)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v14.0.0...v15.0.0)

**Merged pull requests:**

- cram [\#128](https://github.com/sanger-pathogens/Artemis/pull/128) ([tcarver](https://github.com/tcarver))
- misc [\#127](https://github.com/sanger-pathogens/Artemis/pull/127) ([tcarver](https://github.com/tcarver))
- add a log statement  [\#126](https://github.com/sanger-pathogens/Artemis/pull/126) ([tcarver](https://github.com/tcarver))
- misc [\#125](https://github.com/sanger-pathogens/Artemis/pull/125) ([tcarver](https://github.com/tcarver))
- misc [\#124](https://github.com/sanger-pathogens/Artemis/pull/124) ([tcarver](https://github.com/tcarver))
- update [\#123](https://github.com/sanger-pathogens/Artemis/pull/123) ([tcarver](https://github.com/tcarver))
- misc [\#122](https://github.com/sanger-pathogens/Artemis/pull/122) ([tcarver](https://github.com/tcarver))
- misc [\#121](https://github.com/sanger-pathogens/Artemis/pull/121) ([tcarver](https://github.com/tcarver))
- misc [\#120](https://github.com/sanger-pathogens/Artemis/pull/120) ([tcarver](https://github.com/tcarver))
- misc [\#119](https://github.com/sanger-pathogens/Artemis/pull/119) ([tcarver](https://github.com/tcarver))
- misc [\#118](https://github.com/sanger-pathogens/Artemis/pull/118) ([tcarver](https://github.com/tcarver))
- misc [\#117](https://github.com/sanger-pathogens/Artemis/pull/117) ([tcarver](https://github.com/tcarver))
- misc [\#115](https://github.com/sanger-pathogens/Artemis/pull/115) ([tcarver](https://github.com/tcarver))
- batik 1.7 [\#114](https://github.com/sanger-pathogens/Artemis/pull/114) ([tcarver](https://github.com/tcarver))
- misc [\#113](https://github.com/sanger-pathogens/Artemis/pull/113) ([tcarver](https://github.com/tcarver))
- changes for setting partial on featureloc [\#112](https://github.com/sanger-pathogens/Artemis/pull/112) ([tcarver](https://github.com/tcarver))
- misc [\#111](https://github.com/sanger-pathogens/Artemis/pull/111) ([tcarver](https://github.com/tcarver))
- misc [\#110](https://github.com/sanger-pathogens/Artemis/pull/110) ([tcarver](https://github.com/tcarver))
- misc [\#109](https://github.com/sanger-pathogens/Artemis/pull/109) ([tcarver](https://github.com/tcarver))
- misc [\#108](https://github.com/sanger-pathogens/Artemis/pull/108) ([tcarver](https://github.com/tcarver))
- misc [\#107](https://github.com/sanger-pathogens/Artemis/pull/107) ([tcarver](https://github.com/tcarver))
- BamView changes [\#106](https://github.com/sanger-pathogens/Artemis/pull/106) ([tcarver](https://github.com/tcarver))
- misc [\#105](https://github.com/sanger-pathogens/Artemis/pull/105) ([tcarver](https://github.com/tcarver))
- misc [\#104](https://github.com/sanger-pathogens/Artemis/pull/104) ([tcarver](https://github.com/tcarver))
- misc [\#103](https://github.com/sanger-pathogens/Artemis/pull/103) ([tcarver](https://github.com/tcarver))
- add picard libs to classpath [\#102](https://github.com/sanger-pathogens/Artemis/pull/102) ([tcarver](https://github.com/tcarver))
- misc [\#101](https://github.com/sanger-pathogens/Artemis/pull/101) ([tcarver](https://github.com/tcarver))
- misc [\#100](https://github.com/sanger-pathogens/Artemis/pull/100) ([tcarver](https://github.com/tcarver))
- dnaplotter speed up with BLAST files [\#99](https://github.com/sanger-pathogens/Artemis/pull/99) ([tcarver](https://github.com/tcarver))
- update version [\#98](https://github.com/sanger-pathogens/Artemis/pull/98) ([tcarver](https://github.com/tcarver))
- misc [\#97](https://github.com/sanger-pathogens/Artemis/pull/97) ([tcarver](https://github.com/tcarver))
- misc [\#96](https://github.com/sanger-pathogens/Artemis/pull/96) ([tcarver](https://github.com/tcarver))
- update version [\#95](https://github.com/sanger-pathogens/Artemis/pull/95) ([tcarver](https://github.com/tcarver))
- misc [\#94](https://github.com/sanger-pathogens/Artemis/pull/94) ([tcarver](https://github.com/tcarver))
- make executable [\#93](https://github.com/sanger-pathogens/Artemis/pull/93) ([tcarver](https://github.com/tcarver))
- misc [\#92](https://github.com/sanger-pathogens/Artemis/pull/92) ([tcarver](https://github.com/tcarver))
- misc [\#91](https://github.com/sanger-pathogens/Artemis/pull/91) ([tcarver](https://github.com/tcarver))
- misc [\#90](https://github.com/sanger-pathogens/Artemis/pull/90) ([tcarver](https://github.com/tcarver))
- misc [\#89](https://github.com/sanger-pathogens/Artemis/pull/89) ([tcarver](https://github.com/tcarver))
- clear GFF cache [\#88](https://github.com/sanger-pathogens/Artemis/pull/88) ([tcarver](https://github.com/tcarver))
- phase is REQUIRED for all CDS features [\#87](https://github.com/sanger-pathogens/Artemis/pull/87) ([tcarver](https://github.com/tcarver))
- misc [\#86](https://github.com/sanger-pathogens/Artemis/pull/86) ([tcarver](https://github.com/tcarver))
- allow user to open database entry using gene or sequence ID [\#85](https://github.com/sanger-pathogens/Artemis/pull/85) ([tcarver](https://github.com/tcarver))
- misc [\#84](https://github.com/sanger-pathogens/Artemis/pull/84) ([tcarver](https://github.com/tcarver))
- misc [\#83](https://github.com/sanger-pathogens/Artemis/pull/83) ([tcarver](https://github.com/tcarver))
- misc [\#82](https://github.com/sanger-pathogens/Artemis/pull/82) ([tcarver](https://github.com/tcarver))
- misc [\#81](https://github.com/sanger-pathogens/Artemis/pull/81) ([tcarver](https://github.com/tcarver))
- update version [\#80](https://github.com/sanger-pathogens/Artemis/pull/80) ([tcarver](https://github.com/tcarver))
- misc [\#79](https://github.com/sanger-pathogens/Artemis/pull/79) ([tcarver](https://github.com/tcarver))
- fix if etc/project.properties is missing [\#78](https://github.com/sanger-pathogens/Artemis/pull/78) ([tcarver](https://github.com/tcarver))
- fix for BAM index [\#77](https://github.com/sanger-pathogens/Artemis/pull/77) ([tcarver](https://github.com/tcarver))
- update version [\#76](https://github.com/sanger-pathogens/Artemis/pull/76) ([tcarver](https://github.com/tcarver))
- misc [\#75](https://github.com/sanger-pathogens/Artemis/pull/75) ([tcarver](https://github.com/tcarver))
- misc [\#74](https://github.com/sanger-pathogens/Artemis/pull/74) ([tcarver](https://github.com/tcarver))
- change to scratch [\#73](https://github.com/sanger-pathogens/Artemis/pull/73) ([tcarver](https://github.com/tcarver))
- misc [\#72](https://github.com/sanger-pathogens/Artemis/pull/72) ([tcarver](https://github.com/tcarver))
- misc [\#71](https://github.com/sanger-pathogens/Artemis/pull/71) ([tcarver](https://github.com/tcarver))
- misc [\#70](https://github.com/sanger-pathogens/Artemis/pull/70) ([tcarver](https://github.com/tcarver))
- misc [\#69](https://github.com/sanger-pathogens/Artemis/pull/69) ([tcarver](https://github.com/tcarver))
- misc [\#68](https://github.com/sanger-pathogens/Artemis/pull/68) ([tcarver](https://github.com/tcarver))
- update [\#67](https://github.com/sanger-pathogens/Artemis/pull/67) ([tcarver](https://github.com/tcarver))
- feature stack view [\#66](https://github.com/sanger-pathogens/Artemis/pull/66) ([tcarver](https://github.com/tcarver))
- misc [\#65](https://github.com/sanger-pathogens/Artemis/pull/65) ([tcarver](https://github.com/tcarver))
- misc [\#64](https://github.com/sanger-pathogens/Artemis/pull/64) ([tcarver](https://github.com/tcarver))
- misc [\#63](https://github.com/sanger-pathogens/Artemis/pull/63) ([tcarver](https://github.com/tcarver))
- misc [\#62](https://github.com/sanger-pathogens/Artemis/pull/62) ([tcarver](https://github.com/tcarver))
- remove embl suffix from ID in EMBL header [\#61](https://github.com/sanger-pathogens/Artemis/pull/61) ([tcarver](https://github.com/tcarver))
- fix for reading back in user defined shortcuts [\#60](https://github.com/sanger-pathogens/Artemis/pull/60) ([tcarver](https://github.com/tcarver))
- misc [\#59](https://github.com/sanger-pathogens/Artemis/pull/59) ([tcarver](https://github.com/tcarver))
- misc [\#58](https://github.com/sanger-pathogens/Artemis/pull/58) ([tcarver](https://github.com/tcarver))
- misc [\#57](https://github.com/sanger-pathogens/Artemis/pull/57) ([tcarver](https://github.com/tcarver))
- fix for getCDSLine\(\) [\#56](https://github.com/sanger-pathogens/Artemis/pull/56) ([tcarver](https://github.com/tcarver))
- fix for update partial settings [\#55](https://github.com/sanger-pathogens/Artemis/pull/55) ([tcarver](https://github.com/tcarver))
- GFF and feature stack view [\#54](https://github.com/sanger-pathogens/Artemis/pull/54) ([tcarver](https://github.com/tcarver))
- misc GFF support [\#53](https://github.com/sanger-pathogens/Artemis/pull/53) ([tcarver](https://github.com/tcarver))
- misc [\#52](https://github.com/sanger-pathogens/Artemis/pull/52) ([tcarver](https://github.com/tcarver))

## [v14.0.0](https://github.com/sanger-pathogens/artemis/tree/v14.0.0) (2012-02-20)
[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v13.2.0...v14.0.0)

**Merged pull requests:**

- misc [\#51](https://github.com/sanger-pathogens/Artemis/pull/51) ([tcarver](https://github.com/tcarver))
- misc [\#50](https://github.com/sanger-pathogens/Artemis/pull/50) ([tcarver](https://github.com/tcarver))
- VALIDATION\_STRINGENCY=SILENT [\#49](https://github.com/sanger-pathogens/Artemis/pull/49) ([tcarver](https://github.com/tcarver))
- set VALIDATION\_STRINGENCY=LENIENT [\#48](https://github.com/sanger-pathogens/Artemis/pull/48) ([tcarver](https://github.com/tcarver))
- set viewport position for the strand view when changing resolution [\#47](https://github.com/sanger-pathogens/Artemis/pull/47) ([tcarver](https://github.com/tcarver))
- misc [\#46](https://github.com/sanger-pathogens/Artemis/pull/46) ([tcarver](https://github.com/tcarver))
- misc [\#45](https://github.com/sanger-pathogens/Artemis/pull/45) ([tcarver](https://github.com/tcarver))
- add to extra\_keys\_gff [\#44](https://github.com/sanger-pathogens/Artemis/pull/44) ([tcarver](https://github.com/tcarver))
- adding tooltips [\#43](https://github.com/sanger-pathogens/Artemis/pull/43) ([tcarver](https://github.com/tcarver))
- misc [\#42](https://github.com/sanger-pathogens/Artemis/pull/42) ([tcarver](https://github.com/tcarver))
- misc [\#41](https://github.com/sanger-pathogens/Artemis/pull/41) ([tcarver](https://github.com/tcarver))
- misc [\#40](https://github.com/sanger-pathogens/Artemis/pull/40) ([tcarver](https://github.com/tcarver))
- optimise [\#39](https://github.com/sanger-pathogens/Artemis/pull/39) ([tcarver](https://github.com/tcarver))
- fix for VCF file parse\(\) [\#38](https://github.com/sanger-pathogens/Artemis/pull/38) ([tcarver](https://github.com/tcarver))
- vcf updates [\#37](https://github.com/sanger-pathogens/Artemis/pull/37) ([tcarver](https://github.com/tcarver))
- file suffix [\#36](https://github.com/sanger-pathogens/Artemis/pull/36) ([tcarver](https://github.com/tcarver))
- misc bamview and vcfview [\#35](https://github.com/sanger-pathogens/Artemis/pull/35) ([tcarver](https://github.com/tcarver))
- update [\#34](https://github.com/sanger-pathogens/Artemis/pull/34) ([tcarver](https://github.com/tcarver))
- fix for getVcfContainer\(\) [\#33](https://github.com/sanger-pathogens/Artemis/pull/33) ([tcarver](https://github.com/tcarver))
- misc [\#32](https://github.com/sanger-pathogens/Artemis/pull/32) ([tcarver](https://github.com/tcarver))
- update version [\#31](https://github.com/sanger-pathogens/Artemis/pull/31) ([tcarver](https://github.com/tcarver))
- misc [\#30](https://github.com/sanger-pathogens/Artemis/pull/30) ([tcarver](https://github.com/tcarver))
- standalone BamView improvements [\#29](https://github.com/sanger-pathogens/Artemis/pull/29) ([tcarver](https://github.com/tcarver))
- misc [\#28](https://github.com/sanger-pathogens/Artemis/pull/28) ([tcarver](https://github.com/tcarver))
- fix for selenocysteine on reverse strand [\#27](https://github.com/sanger-pathogens/Artemis/pull/27) ([tcarver](https://github.com/tcarver))
- misc [\#26](https://github.com/sanger-pathogens/Artemis/pull/26) ([tcarver](https://github.com/tcarver))
- fix VCF test [\#25](https://github.com/sanger-pathogens/Artemis/pull/25) ([tcarver](https://github.com/tcarver))
- misc [\#24](https://github.com/sanger-pathogens/Artemis/pull/24) ([tcarver](https://github.com/tcarver))
- shortcut changed in Preferences are saved between sessions [\#23](https://github.com/sanger-pathogens/Artemis/pull/23) ([tcarver](https://github.com/tcarver))
- work around for backward compatibility with old BCF files [\#22](https://github.com/sanger-pathogens/Artemis/pull/22) ([tcarver](https://github.com/tcarver))
- changed to use SHIFT to drag ends when zoomed out [\#21](https://github.com/sanger-pathogens/Artemis/pull/21) ([tcarver](https://github.com/tcarver))
- alt key used to drag ends when zoomed out and fix for loading multiple artemis windos [\#20](https://github.com/sanger-pathogens/Artemis/pull/20) ([tcarver](https://github.com/tcarver))
- change handleSelenocysteine [\#19](https://github.com/sanger-pathogens/Artemis/pull/19) ([tcarver](https://github.com/tcarver))
- GTF fixes [\#18](https://github.com/sanger-pathogens/Artemis/pull/18) ([tcarver](https://github.com/tcarver))
- various [\#17](https://github.com/sanger-pathogens/Artemis/pull/17) ([tcarver](https://github.com/tcarver))
- update version [\#16](https://github.com/sanger-pathogens/Artemis/pull/16) ([tcarver](https://github.com/tcarver))
- typo [\#15](https://github.com/sanger-pathogens/Artemis/pull/15) ([tcarver](https://github.com/tcarver))
- fix for partials and use non-modal to report reference change [\#14](https://github.com/sanger-pathogens/Artemis/pull/14) ([tcarver](https://github.com/tcarver))
- use arrows for partials and fix for UTR ordering [\#13](https://github.com/sanger-pathogens/Artemis/pull/13) ([tcarver](https://github.com/tcarver))
- update version [\#12](https://github.com/sanger-pathogens/Artemis/pull/12) ([tcarver](https://github.com/tcarver))
- changes to allow for loading graphs into ACT from the command line with -DuserplotX system properties [\#11](https://github.com/sanger-pathogens/Artemis/pull/11) ([tcarver](https://github.com/tcarver))
- change default GO db\_xref to GO\_REF:0000001 [\#10](https://github.com/sanger-pathogens/Artemis/pull/10) ([tcarver](https://github.com/tcarver))
- load BAM/VCF files from the command line and SAM record listing [\#9](https://github.com/sanger-pathogens/Artemis/pull/9) ([tcarver](https://github.com/tcarver))
- minor changes to vcf record methods added and fix for list of files on ftp sites [\#8](https://github.com/sanger-pathogens/Artemis/pull/8) ([tcarver](https://github.com/tcarver))
- add mate details and update picard [\#7](https://github.com/sanger-pathogens/Artemis/pull/7) ([tcarver](https://github.com/tcarver))
- Crawl compatability [\#6](https://github.com/sanger-pathogens/Artemis/pull/6) ([buggyvelarde](https://github.com/buggyvelarde))
- TAT and BamView changes [\#5](https://github.com/sanger-pathogens/Artemis/pull/5) ([tcarver](https://github.com/tcarver))
- 2 commits [\#4](https://github.com/sanger-pathogens/Artemis/pull/4) ([tcarver](https://github.com/tcarver))
- update to 13.2.1 [\#3](https://github.com/sanger-pathogens/Artemis/pull/3) ([tcarver](https://github.com/tcarver))

## [v13.2.0](https://github.com/sanger-pathogens/artemis/tree/v13.2.0) (2011-07-13)
**Merged pull requests:**

- update readme [\#2](https://github.com/sanger-pathogens/Artemis/pull/2) ([tcarver](https://github.com/tcarver))



\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
