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CHANGELOG.md  view on Meta::CPAN

[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4)

**Merged pull requests:**

- File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage))
- version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage))

## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3)

**Merged pull requests:**

- Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage))
- Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage))
- Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage))

## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16)
**Merged pull requests:**

- Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage))
- Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins))
- Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage))
- Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage))
- rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage))
- Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage))
- remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage))
- Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage))
- Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins))
- QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins))
- increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage))
- Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage))
- Queue set to basement if number of samples \> 600 \(previously 800\) [\#84](https://github.com/sanger-pathogens/Roary/pull/84) ([carlacummins](https://github.com/carlacummins))
- Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins))
- Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins))
- Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins))
- Multifastas not created when group limit \(default 8000\) exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins))
- allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage))
- increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage))
- Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage))
- Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins))
- Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1))
- if theres more than 1k samples use basement for default analysis [\#74](https://github.com/sanger-pathogens/Roary/pull/74) ([andrewjpage](https://github.com/andrewjpage))
- use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage))
- core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage))
- Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage))
- Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage))
- Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage))
- update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage))
- Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage))
- make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage))
- script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage))
- rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage))
- Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage))
- Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage))
- make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage))
- query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage))
- fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage))
- Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage))
- add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage))
- set the known gene names to black and rest to colours [\#56](https://github.com/sanger-pathogens/Roary/pull/56) ([andrewjpage](https://github.com/andrewjpage))
- print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage))
- Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage))
- fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage))
- Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage))
- Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage))
- pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage))
- iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage))
- Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage))
- Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage))
- dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage))
- rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage))
- cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage))
- Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage))
- align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage))
- Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage))
- Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage))
- Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage))
- Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage))
- split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage))
- make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage))
- dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage))
- run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage))
- annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage))
- Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage))
- Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage))
- remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage))
- blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage))
- Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage))
- Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage))
- Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage))
- use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage))
- renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter))
- GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage))
- lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage))
- low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage))
- inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage))
- report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage))
- update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage))
- speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage))
- sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage))
- create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage))
- Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage))
- Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage))
- check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage))
- catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage))
- tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage))
- label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage))
- extract proteomes from gffs and transfer anntotation as part of script [\#8](https://github.com/sanger-pathogens/Roary/pull/8) ([andrewjpage](https://github.com/andrewjpage))
- transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage))
- speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage))
- typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage))
- run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage))
- vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage))
- working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage))
- Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage))