Mercurial > repos > dereeper > roary_plots
comparison Roary/CHANGELOG.md @ 0:c47a5f61bc9f draft
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| author | dereeper |
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| date | Fri, 14 May 2021 20:27:06 +0000 |
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| 1 # Change Log | |
| 2 | |
| 3 ## [Unreleased](https://github.com/sanger-pathogens/Roary/tree/HEAD) | |
| 4 | |
| 5 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.12.0...HEAD) | |
| 6 | |
| 7 **Implemented enhancements:** | |
| 8 | |
| 9 - Feature Request: Clear error message for duplicated file names [\#363](https://github.com/sanger-pathogens/Roary/issues/363) | |
| 10 | |
| 11 **Fixed bugs:** | |
| 12 | |
| 13 - uninitialized value warning [\#297](https://github.com/sanger-pathogens/Roary/issues/297) | |
| 14 - Bio::Root::Exception thrown during core genome alignment, missing some sequence in core\_gene\_alignment.aln [\#224](https://github.com/sanger-pathogens/Roary/issues/224) | |
| 15 | |
| 16 **Closed issues:** | |
| 17 | |
| 18 - Interpretation accessory\_binary\_genes newick [\#429](https://github.com/sanger-pathogens/Roary/issues/429) | |
| 19 - No gene annotation in gene\_presence\_absence.csv output [\#428](https://github.com/sanger-pathogens/Roary/issues/428) | |
| 20 - Compilation aborted at pan\_genome\_post\_analysis [\#427](https://github.com/sanger-pathogens/Roary/issues/427) | |
| 21 - Could not obtain pan\_genome\_sequences [\#426](https://github.com/sanger-pathogens/Roary/issues/426) | |
| 22 - Pan genome for fungal genomes [\#425](https://github.com/sanger-pathogens/Roary/issues/425) | |
| 23 - multifasta for all proteins [\#424](https://github.com/sanger-pathogens/Roary/issues/424) | |
| 24 - roary\_plots.py KeyError: "X" not in index [\#423](https://github.com/sanger-pathogens/Roary/issues/423) | |
| 25 - Confirm that use of BLAST's `-max\_target\_seqs` is intentional [\#422](https://github.com/sanger-pathogens/Roary/issues/422) | |
| 26 - query\_pan\_genome 'Cant access file' error \(Non-Working-Directory inputs\) [\#421](https://github.com/sanger-pathogens/Roary/issues/421) | |
| 27 - How many .gff files does Roary need? [\#419](https://github.com/sanger-pathogens/Roary/issues/419) | |
| 28 - Installation through Bioconda not working [\#418](https://github.com/sanger-pathogens/Roary/issues/418) | |
| 29 - Is it possible to run roary without prokka output files? [\#417](https://github.com/sanger-pathogens/Roary/issues/417) | |
| 30 - Exiting early because number of clusters is too high [\#415](https://github.com/sanger-pathogens/Roary/issues/415) | |
| 31 - MSG: Got a sequence without letters. Could not guess alphabet? [\#414](https://github.com/sanger-pathogens/Roary/issues/414) | |
| 32 - Which is the advantage to pre-use prokka to perform analysis using genbank \(.gbk and gbff\) files? [\#412](https://github.com/sanger-pathogens/Roary/issues/412) | |
| 33 - issues with running and empty files [\#411](https://github.com/sanger-pathogens/Roary/issues/411) | |
| 34 - MSG: Got a sequence without letters. Could not guess alphabet [\#410](https://github.com/sanger-pathogens/Roary/issues/410) | |
| 35 - moose.pm issue [\#407](https://github.com/sanger-pathogens/Roary/issues/407) | |
| 36 - Tutorial data: extract\_proteome\_from\_gff [\#406](https://github.com/sanger-pathogens/Roary/issues/406) | |
| 37 - Tutorial data: extract\_proteome\_from\_gff [\#403](https://github.com/sanger-pathogens/Roary/issues/403) | |
| 38 - gene\_presence\_absence.csv incomplete [\#402](https://github.com/sanger-pathogens/Roary/issues/402) | |
| 39 - Roary including non-protein coding features? [\#398](https://github.com/sanger-pathogens/Roary/issues/398) | |
| 40 - Question: what programs can be used to visualize embl and dot files? [\#394](https://github.com/sanger-pathogens/Roary/issues/394) | |
| 41 - Roary Does not terminated successfully [\#388](https://github.com/sanger-pathogens/Roary/issues/388) | |
| 42 - python: can't open file 'roary\_plots.py': \[Errno 2\] No such file or directory [\#385](https://github.com/sanger-pathogens/Roary/issues/385) | |
| 43 - Roary does not finish analysis even though cluster job queue returns successful completion [\#383](https://github.com/sanger-pathogens/Roary/issues/383) | |
| 44 - Genes \(well\) annotated in prokka end up all in different groups?? [\#355](https://github.com/sanger-pathogens/Roary/issues/355) | |
| 45 - could not determine version of cd-hit [\#322](https://github.com/sanger-pathogens/Roary/issues/322) | |
| 46 - Use of uninitialized value in require at \(eval 792\) line 1. [\#308](https://github.com/sanger-pathogens/Roary/issues/308) | |
| 47 - Error: unexpected input in "\_" [\#299](https://github.com/sanger-pathogens/Roary/issues/299) | |
| 48 - inconsistent referencing of $TMPDIR ? [\#287](https://github.com/sanger-pathogens/Roary/issues/287) | |
| 49 | |
| 50 **Merged pull requests:** | |
| 51 | |
| 52 - Include tests in README [\#430](https://github.com/sanger-pathogens/Roary/pull/430) ([ssjunnebo](https://github.com/ssjunnebo)) | |
| 53 - 621556 badges [\#420](https://github.com/sanger-pathogens/Roary/pull/420) ([ssjunnebo](https://github.com/ssjunnebo)) | |
| 54 - Update roary\_plots from .ix to .loc [\#416](https://github.com/sanger-pathogens/Roary/pull/416) ([EvdH0](https://github.com/EvdH0)) | |
| 55 - Use only CDS features from GFF [\#400](https://github.com/sanger-pathogens/Roary/pull/400) ([embatty](https://github.com/embatty)) | |
| 56 - also mention Devel::OverloadInfo and Digest::MD5::File as required Perl dependencies [\#397](https://github.com/sanger-pathogens/Roary/pull/397) ([boegel](https://github.com/boegel)) | |
| 57 - Avoid deprecation errors in roary\_plots [\#389](https://github.com/sanger-pathogens/Roary/pull/389) ([mgalardini](https://github.com/mgalardini)) | |
| 58 | |
| 59 ## [v3.12.0](https://github.com/sanger-pathogens/Roary/tree/v3.12.0) (2018-01-23) | |
| 60 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.4...v3.12.0) | |
| 61 | |
| 62 **Merged pull requests:** | |
| 63 | |
| 64 - Reduce min gene size [\#384](https://github.com/sanger-pathogens/Roary/pull/384) ([ssjunnebo](https://github.com/ssjunnebo)) | |
| 65 | |
| 66 ## [v3.11.4](https://github.com/sanger-pathogens/Roary/tree/v3.11.4) (2018-01-16) | |
| 67 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.3...v3.11.4) | |
| 68 | |
| 69 **Closed issues:** | |
| 70 | |
| 71 - Roary seemed to have stopped prematurely; any way to continue the run? [\#380](https://github.com/sanger-pathogens/Roary/issues/380) | |
| 72 - Getting prank version without the online check [\#377](https://github.com/sanger-pathogens/Roary/issues/377) | |
| 73 - Kraken version parsing error: [\#376](https://github.com/sanger-pathogens/Roary/issues/376) | |
| 74 - 3.11.1 failing 2/55 \(3/791\) tests [\#375](https://github.com/sanger-pathogens/Roary/issues/375) | |
| 75 - Fix for prank version check [\#361](https://github.com/sanger-pathogens/Roary/issues/361) | |
| 76 - mafft version check still failing - bug in regexp found [\#360](https://github.com/sanger-pathogens/Roary/issues/360) | |
| 77 - roary -a =\> Use of uninitialized value in concatenation \(.\) [\#270](https://github.com/sanger-pathogens/Roary/issues/270) | |
| 78 | |
| 79 **Merged pull requests:** | |
| 80 | |
| 81 - Fix dependancy checking option [\#382](https://github.com/sanger-pathogens/Roary/pull/382) ([andrewjpage](https://github.com/andrewjpage)) | |
| 82 | |
| 83 ## [v3.11.3](https://github.com/sanger-pathogens/Roary/tree/v3.11.3) (2018-01-12) | |
| 84 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.2...v3.11.3) | |
| 85 | |
| 86 **Merged pull requests:** | |
| 87 | |
| 88 - Version fix [\#379](https://github.com/sanger-pathogens/Roary/pull/379) ([andrewjpage](https://github.com/andrewjpage)) | |
| 89 | |
| 90 ## [v3.11.2](https://github.com/sanger-pathogens/Roary/tree/v3.11.2) (2018-01-12) | |
| 91 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.1...v3.11.2) | |
| 92 | |
| 93 **Fixed bugs:** | |
| 94 | |
| 95 - ExtractProteomeFromGff.t failing tests 3.11.0 [\#373](https://github.com/sanger-pathogens/Roary/issues/373) | |
| 96 | |
| 97 **Merged pull requests:** | |
| 98 | |
| 99 - fix mafft and kraken version extraction [\#378](https://github.com/sanger-pathogens/Roary/pull/378) ([andrewjpage](https://github.com/andrewjpage)) | |
| 100 | |
| 101 ## [v3.11.1](https://github.com/sanger-pathogens/Roary/tree/v3.11.1) (2018-01-10) | |
| 102 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.0...v3.11.1) | |
| 103 | |
| 104 **Closed issues:** | |
| 105 | |
| 106 - Sorting in version 3.11.0: uppercase letters first, lowercase second \(non-alphabetical\) [\#371](https://github.com/sanger-pathogens/Roary/issues/371) | |
| 107 - Genbank input [\#365](https://github.com/sanger-pathogens/Roary/issues/365) | |
| 108 - not all annotated features are allocated to the clusters [\#359](https://github.com/sanger-pathogens/Roary/issues/359) | |
| 109 | |
| 110 **Merged pull requests:** | |
| 111 | |
| 112 - Bedtools getfasta format fix [\#374](https://github.com/sanger-pathogens/Roary/pull/374) ([andrewjpage](https://github.com/andrewjpage)) | |
| 113 - Update roary\_plots.py [\#372](https://github.com/sanger-pathogens/Roary/pull/372) ([franz89](https://github.com/franz89)) | |
| 114 - Issue \#363 add check for duplicate basenames [\#370](https://github.com/sanger-pathogens/Roary/pull/370) ([nickp60](https://github.com/nickp60)) | |
| 115 - README.md: Update Guix install instructions. [\#362](https://github.com/sanger-pathogens/Roary/pull/362) ([wwood](https://github.com/wwood)) | |
| 116 | |
| 117 ## [v3.11.0](https://github.com/sanger-pathogens/Roary/tree/v3.11.0) (2017-10-10) | |
| 118 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.2...v3.11.0) | |
| 119 | |
| 120 **Fixed bugs:** | |
| 121 | |
| 122 - Can't get version of kraken, kraken-report or mafft ? [\#312](https://github.com/sanger-pathogens/Roary/issues/312) | |
| 123 | |
| 124 **Closed issues:** | |
| 125 | |
| 126 - number\_of\_conserved\_genes.Rtab [\#354](https://github.com/sanger-pathogens/Roary/issues/354) | |
| 127 - \[question\] Should it take this long? [\#352](https://github.com/sanger-pathogens/Roary/issues/352) | |
| 128 | |
| 129 **Merged pull requests:** | |
| 130 | |
| 131 - change missing gene in core to be dashes rather than Ns [\#358](https://github.com/sanger-pathogens/Roary/pull/358) ([andrewjpage](https://github.com/andrewjpage)) | |
| 132 | |
| 133 ## [v3.10.2](https://github.com/sanger-pathogens/Roary/tree/v3.10.2) (2017-09-08) | |
| 134 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.1...v3.10.2) | |
| 135 | |
| 136 **Closed issues:** | |
| 137 | |
| 138 - \[version 3.8.0\] Roary crashes at end on perl error message [\#323](https://github.com/sanger-pathogens/Roary/issues/323) | |
| 139 - Cant open file: \_accessory\_clusters.clstr [\#320](https://github.com/sanger-pathogens/Roary/issues/320) | |
| 140 | |
| 141 **Merged pull requests:** | |
| 142 | |
| 143 - get kraken version [\#351](https://github.com/sanger-pathogens/Roary/pull/351) ([andrewjpage](https://github.com/andrewjpage)) | |
| 144 | |
| 145 ## [v3.10.1](https://github.com/sanger-pathogens/Roary/tree/v3.10.1) (2017-09-07) | |
| 146 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.0...v3.10.1) | |
| 147 | |
| 148 **Implemented enhancements:** | |
| 149 | |
| 150 - Auto-detect if input files are GFF or FASTA [\#348](https://github.com/sanger-pathogens/Roary/issues/348) | |
| 151 - Can "Fixing input GFF files" be parallelized? [\#342](https://github.com/sanger-pathogens/Roary/issues/342) | |
| 152 | |
| 153 **Fixed bugs:** | |
| 154 | |
| 155 - The GNU General Public License, Version not specified [\#344](https://github.com/sanger-pathogens/Roary/issues/344) | |
| 156 | |
| 157 **Closed issues:** | |
| 158 | |
| 159 - MSG: The sequence does not appear to be FASTA format \(lacks a descriptor line '\>'\) [\#346](https://github.com/sanger-pathogens/Roary/issues/346) | |
| 160 | |
| 161 **Merged pull requests:** | |
| 162 | |
| 163 - Improve input file handling [\#350](https://github.com/sanger-pathogens/Roary/pull/350) ([andrewjpage](https://github.com/andrewjpage)) | |
| 164 | |
| 165 ## [v3.10.0](https://github.com/sanger-pathogens/Roary/tree/v3.10.0) (2017-09-07) | |
| 166 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.1...v3.10.0) | |
| 167 | |
| 168 **Closed issues:** | |
| 169 | |
| 170 - Use of uninitialized value \(Perl\) [\#345](https://github.com/sanger-pathogens/Roary/issues/345) | |
| 171 - identical .gff file names from different genome, and then issue with mcl groups [\#341](https://github.com/sanger-pathogens/Roary/issues/341) | |
| 172 - Cant open file: \_clustered.clstr [\#339](https://github.com/sanger-pathogens/Roary/issues/339) | |
| 173 | |
| 174 ## [v3.9.1](https://github.com/sanger-pathogens/Roary/tree/v3.9.1) (2017-08-22) | |
| 175 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.0...v3.9.1) | |
| 176 | |
| 177 **Merged pull requests:** | |
| 178 | |
| 179 - Optionally allow paralogs in core gene alignment [\#343](https://github.com/sanger-pathogens/Roary/pull/343) ([andrewjpage](https://github.com/andrewjpage)) | |
| 180 - Script to find frequency of unique genes in samples [\#340](https://github.com/sanger-pathogens/Roary/pull/340) ([andrewjpage](https://github.com/andrewjpage)) | |
| 181 | |
| 182 ## [v3.9.0](https://github.com/sanger-pathogens/Roary/tree/v3.9.0) (2017-08-09) | |
| 183 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.2...v3.9.0) | |
| 184 | |
| 185 **Closed issues:** | |
| 186 | |
| 187 - roary\_plots: pangenome matrix tree does not look like input.newick tree [\#333](https://github.com/sanger-pathogens/Roary/issues/333) | |
| 188 - use Roary with RAST files [\#332](https://github.com/sanger-pathogens/Roary/issues/332) | |
| 189 - Roary [\#329](https://github.com/sanger-pathogens/Roary/issues/329) | |
| 190 - sampling number is 10 in number of genes in pan and core genome [\#319](https://github.com/sanger-pathogens/Roary/issues/319) | |
| 191 | |
| 192 **Merged pull requests:** | |
| 193 | |
| 194 - Grammar edits [\#327](https://github.com/sanger-pathogens/Roary/pull/327) ([cgreene](https://github.com/cgreene)) | |
| 195 - allow for inflation factor for MCL to be changed [\#326](https://github.com/sanger-pathogens/Roary/pull/326) ([andrewjpage](https://github.com/andrewjpage)) | |
| 196 | |
| 197 ## [v3.8.2](https://github.com/sanger-pathogens/Roary/tree/v3.8.2) (2017-05-21) | |
| 198 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.1...v3.8.2) | |
| 199 | |
| 200 ## [v3.8.1](https://github.com/sanger-pathogens/Roary/tree/v3.8.1) (2017-05-21) | |
| 201 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.0...v3.8.1) | |
| 202 | |
| 203 **Closed issues:** | |
| 204 | |
| 205 - BLAST Database error [\#321](https://github.com/sanger-pathogens/Roary/issues/321) | |
| 206 - Results for same input differ always a bit \(summary\_statistics.txt\) [\#318](https://github.com/sanger-pathogens/Roary/issues/318) | |
| 207 - Error: Couldnt open GFF file [\#314](https://github.com/sanger-pathogens/Roary/issues/314) | |
| 208 - Help with query\_pan\_genome [\#313](https://github.com/sanger-pathogens/Roary/issues/313) | |
| 209 | |
| 210 **Merged pull requests:** | |
| 211 | |
| 212 - update email address [\#325](https://github.com/sanger-pathogens/Roary/pull/325) ([ssjunnebo](https://github.com/ssjunnebo)) | |
| 213 - New option to roary\_plots.py [\#317](https://github.com/sanger-pathogens/Roary/pull/317) ([mgalardini](https://github.com/mgalardini)) | |
| 214 | |
| 215 ## [v3.8.0](https://github.com/sanger-pathogens/Roary/tree/v3.8.0) (2017-01-25) | |
| 216 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.1...v3.8.0) | |
| 217 | |
| 218 **Closed issues:** | |
| 219 | |
| 220 - Old version in the master tarball? [\#300](https://github.com/sanger-pathogens/Roary/issues/300) | |
| 221 - prank is not installed \(Linuxbrew\) [\#294](https://github.com/sanger-pathogens/Roary/issues/294) | |
| 222 - roary\_plots.py problem [\#292](https://github.com/sanger-pathogens/Roary/issues/292) | |
| 223 | |
| 224 **Merged pull requests:** | |
| 225 | |
| 226 - Support latest version of blast [\#306](https://github.com/sanger-pathogens/Roary/pull/306) ([andrewjpage](https://github.com/andrewjpage)) | |
| 227 - infgen [\#305](https://github.com/sanger-pathogens/Roary/pull/305) ([andrewjpage](https://github.com/andrewjpage)) | |
| 228 - update from 108 to 118 [\#304](https://github.com/sanger-pathogens/Roary/pull/304) ([andrewjpage](https://github.com/andrewjpage)) | |
| 229 - update usage text for iterative CD-hit [\#301](https://github.com/sanger-pathogens/Roary/pull/301) ([andrewjpage](https://github.com/andrewjpage)) | |
| 230 | |
| 231 ## [v3.7.1](https://github.com/sanger-pathogens/Roary/tree/v3.7.1) (2016-11-01) | |
| 232 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.0...v3.7.1) | |
| 233 | |
| 234 **Closed issues:** | |
| 235 | |
| 236 - core\_gene\_alignment.aln missing [\#284](https://github.com/sanger-pathogens/Roary/issues/284) | |
| 237 - Is these results fine to use? [\#282](https://github.com/sanger-pathogens/Roary/issues/282) | |
| 238 | |
| 239 **Merged pull requests:** | |
| 240 | |
| 241 - fix spelling [\#280](https://github.com/sanger-pathogens/Roary/pull/280) ([satta](https://github.com/satta)) | |
| 242 - dont add POD to end of R scripts [\#279](https://github.com/sanger-pathogens/Roary/pull/279) ([andrewjpage](https://github.com/andrewjpage)) | |
| 243 | |
| 244 ## [v3.7.0](https://github.com/sanger-pathogens/Roary/tree/v3.7.0) (2016-09-23) | |
| 245 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.9...v3.7.0) | |
| 246 | |
| 247 ## [v3.6.9](https://github.com/sanger-pathogens/Roary/tree/v3.6.9) (2016-09-22) | |
| 248 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.8...v3.6.9) | |
| 249 | |
| 250 **Implemented enhancements:** | |
| 251 | |
| 252 - I have published a Roary homebrew formula [\#208](https://github.com/sanger-pathogens/Roary/issues/208) | |
| 253 - Getting Roary into Homebrew [\#152](https://github.com/sanger-pathogens/Roary/issues/152) | |
| 254 | |
| 255 **Closed issues:** | |
| 256 | |
| 257 - roary\_plots.py missing [\#277](https://github.com/sanger-pathogens/Roary/issues/277) | |
| 258 - Errors when downloaded sequences from NCBI [\#274](https://github.com/sanger-pathogens/Roary/issues/274) | |
| 259 - Same dataset different results! [\#271](https://github.com/sanger-pathogens/Roary/issues/271) | |
| 260 - \_clustered.clstr file does not exist, cannot be read [\#250](https://github.com/sanger-pathogens/Roary/issues/250) | |
| 261 | |
| 262 **Merged pull requests:** | |
| 263 | |
| 264 - Fixed easy-init warnings - 529655 [\#278](https://github.com/sanger-pathogens/Roary/pull/278) ([psweston](https://github.com/psweston)) | |
| 265 - README.md: Add instructions for GNU Guix. [\#273](https://github.com/sanger-pathogens/Roary/pull/273) ([wwood](https://github.com/wwood)) | |
| 266 | |
| 267 ## [v3.6.8](https://github.com/sanger-pathogens/Roary/tree/v3.6.8) (2016-08-02) | |
| 268 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.7...v3.6.8) | |
| 269 | |
| 270 **Merged pull requests:** | |
| 271 | |
| 272 - Allow gene names from gb [\#266](https://github.com/sanger-pathogens/Roary/pull/266) ([andrewjpage](https://github.com/andrewjpage)) | |
| 273 - Missing genes [\#265](https://github.com/sanger-pathogens/Roary/pull/265) ([andrewjpage](https://github.com/andrewjpage)) | |
| 274 | |
| 275 ## [v3.6.7](https://github.com/sanger-pathogens/Roary/tree/v3.6.7) (2016-07-26) | |
| 276 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.6...v3.6.7) | |
| 277 | |
| 278 **Fixed bugs:** | |
| 279 | |
| 280 - Roary 3.6.5 giving different \(erroneous\) results compared to 3.5.7 and 3.6.1/3.6.3/3.6.4 [\#263](https://github.com/sanger-pathogens/Roary/issues/263) | |
| 281 - roary R plots don't work on server --- lack of X11 [\#194](https://github.com/sanger-pathogens/Roary/issues/194) | |
| 282 | |
| 283 **Closed issues:** | |
| 284 | |
| 285 - empty accessory\_binary\_genes.fa file [\#262](https://github.com/sanger-pathogens/Roary/issues/262) | |
| 286 - a guix package [\#259](https://github.com/sanger-pathogens/Roary/issues/259) | |
| 287 - create\_pan\_genome\_plots.R - X11 font problem [\#230](https://github.com/sanger-pathogens/Roary/issues/230) | |
| 288 - Roary not generating pan\_genome\_reference.fa [\#223](https://github.com/sanger-pathogens/Roary/issues/223) | |
| 289 - Roary not using packaged executables [\#215](https://github.com/sanger-pathogens/Roary/issues/215) | |
| 290 | |
| 291 ## [v3.6.6](https://github.com/sanger-pathogens/Roary/tree/v3.6.6) (2016-07-25) | |
| 292 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.5...v3.6.6) | |
| 293 | |
| 294 **Fixed bugs:** | |
| 295 | |
| 296 - GFF parsing doesn't match GFF3 specification [\#249](https://github.com/sanger-pathogens/Roary/issues/249) | |
| 297 | |
| 298 **Merged pull requests:** | |
| 299 | |
| 300 - Fix empty accessory binary [\#264](https://github.com/sanger-pathogens/Roary/pull/264) ([andrewjpage](https://github.com/andrewjpage)) | |
| 301 - change to dist zilla starter bundle [\#261](https://github.com/sanger-pathogens/Roary/pull/261) ([nds](https://github.com/nds)) | |
| 302 | |
| 303 ## [v3.6.5](https://github.com/sanger-pathogens/Roary/tree/v3.6.5) (2016-07-20) | |
| 304 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.4...v3.6.5) | |
| 305 | |
| 306 **Merged pull requests:** | |
| 307 | |
| 308 - allow new format bedtools and dont look for FASTA in GFF [\#260](https://github.com/sanger-pathogens/Roary/pull/260) ([andrewjpage](https://github.com/andrewjpage)) | |
| 309 - catch divide by zero error [\#258](https://github.com/sanger-pathogens/Roary/pull/258) ([andrewjpage](https://github.com/andrewjpage)) | |
| 310 | |
| 311 ## [v3.6.4](https://github.com/sanger-pathogens/Roary/tree/v3.6.4) (2016-07-06) | |
| 312 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.3...v3.6.4) | |
| 313 | |
| 314 **Merged pull requests:** | |
| 315 | |
| 316 - drop testing for perl 5.10, add 5.24. dzil no longer works below 5.14 [\#257](https://github.com/sanger-pathogens/Roary/pull/257) ([andrewjpage](https://github.com/andrewjpage)) | |
| 317 | |
| 318 ## [v3.6.3](https://github.com/sanger-pathogens/Roary/tree/v3.6.3) (2016-07-01) | |
| 319 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.2...v3.6.3) | |
| 320 | |
| 321 **Merged pull requests:** | |
| 322 | |
| 323 - Speed up alignments [\#256](https://github.com/sanger-pathogens/Roary/pull/256) ([andrewjpage](https://github.com/andrewjpage)) | |
| 324 | |
| 325 ## [v3.6.2](https://github.com/sanger-pathogens/Roary/tree/v3.6.2) (2016-05-10) | |
| 326 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.1...v3.6.2) | |
| 327 | |
| 328 **Implemented enhancements:** | |
| 329 | |
| 330 - Prefix utility commands with roary- ? [\#226](https://github.com/sanger-pathogens/Roary/issues/226) | |
| 331 | |
| 332 **Merged pull requests:** | |
| 333 | |
| 334 - fix bug Can't exec /bin/sh: Argument list too long [\#247](https://github.com/sanger-pathogens/Roary/pull/247) ([duytintruong](https://github.com/duytintruong)) | |
| 335 - get rid of warning message [\#246](https://github.com/sanger-pathogens/Roary/pull/246) ([satta](https://github.com/satta)) | |
| 336 | |
| 337 ## [v3.6.1](https://github.com/sanger-pathogens/Roary/tree/v3.6.1) (2016-04-18) | |
| 338 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.0...v3.6.1) | |
| 339 | |
| 340 **Fixed bugs:** | |
| 341 | |
| 342 - roary\_plots.py generating flawed plots [\#221](https://github.com/sanger-pathogens/Roary/issues/221) | |
| 343 | |
| 344 **Closed issues:** | |
| 345 | |
| 346 - Core gene file missing error [\#241](https://github.com/sanger-pathogens/Roary/issues/241) | |
| 347 | |
| 348 **Merged pull requests:** | |
| 349 | |
| 350 - prefix commands with roary [\#244](https://github.com/sanger-pathogens/Roary/pull/244) ([andrewjpage](https://github.com/andrewjpage)) | |
| 351 - More improvements to roary\_plots [\#240](https://github.com/sanger-pathogens/Roary/pull/240) ([mgalardini](https://github.com/mgalardini)) | |
| 352 | |
| 353 ## [v3.6.0](https://github.com/sanger-pathogens/Roary/tree/v3.6.0) (2016-02-23) | |
| 354 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.9...v3.6.0) | |
| 355 | |
| 356 **Fixed bugs:** | |
| 357 | |
| 358 - MSG: Got a sequence without letters. Could not guess alphabet [\#229](https://github.com/sanger-pathogens/Roary/issues/229) | |
| 359 | |
| 360 **Closed issues:** | |
| 361 | |
| 362 - Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? [\#234](https://github.com/sanger-pathogens/Roary/issues/234) | |
| 363 - How to use multiple switches in commandline? [\#232](https://github.com/sanger-pathogens/Roary/issues/232) | |
| 364 | |
| 365 **Merged pull requests:** | |
| 366 | |
| 367 - Improvements to roary\_plots [\#236](https://github.com/sanger-pathogens/Roary/pull/236) ([mgalardini](https://github.com/mgalardini)) | |
| 368 - Rollback 3 5 8 [\#235](https://github.com/sanger-pathogens/Roary/pull/235) ([andrewjpage](https://github.com/andrewjpage)) | |
| 369 | |
| 370 ## [v3.5.9](https://github.com/sanger-pathogens/Roary/tree/v3.5.9) (2016-02-17) | |
| 371 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.8...v3.5.9) | |
| 372 | |
| 373 **Implemented enhancements:** | |
| 374 | |
| 375 - What clusters end up in gene accessory\_binary\_genes.fa ? [\#225](https://github.com/sanger-pathogens/Roary/issues/225) | |
| 376 | |
| 377 **Closed issues:** | |
| 378 | |
| 379 - roary.github.io just prints HELLO [\#233](https://github.com/sanger-pathogens/Roary/issues/233) | |
| 380 | |
| 381 **Merged pull requests:** | |
| 382 | |
| 383 - Fix minor typo [\#231](https://github.com/sanger-pathogens/Roary/pull/231) ([abremges](https://github.com/abremges)) | |
| 384 | |
| 385 ## [v3.5.8](https://github.com/sanger-pathogens/Roary/tree/v3.5.8) (2016-01-20) | |
| 386 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.7...v3.5.8) | |
| 387 | |
| 388 **Implemented enhancements:** | |
| 389 | |
| 390 - Getting Roary into Debian Med [\#219](https://github.com/sanger-pathogens/Roary/issues/219) | |
| 391 - Add embl output file mapping location of each core gene in the core genome alignment [\#192](https://github.com/sanger-pathogens/Roary/issues/192) | |
| 392 | |
| 393 **Closed issues:** | |
| 394 | |
| 395 - Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH [\#217](https://github.com/sanger-pathogens/Roary/issues/217) | |
| 396 | |
| 397 **Merged pull requests:** | |
| 398 | |
| 399 - Provide full accessory for building binary tree [\#227](https://github.com/sanger-pathogens/Roary/pull/227) ([andrewjpage](https://github.com/andrewjpage)) | |
| 400 - roary\_plots: new fields in roary output must be parsed away [\#222](https://github.com/sanger-pathogens/Roary/pull/222) ([mgalardini](https://github.com/mgalardini)) | |
| 401 - Debian nitpicks [\#220](https://github.com/sanger-pathogens/Roary/pull/220) ([satta](https://github.com/satta)) | |
| 402 - Core alignment header file [\#218](https://github.com/sanger-pathogens/Roary/pull/218) ([andrewjpage](https://github.com/andrewjpage)) | |
| 403 | |
| 404 ## [v3.5.7](https://github.com/sanger-pathogens/Roary/tree/v3.5.7) (2015-12-17) | |
| 405 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.6...v3.5.7) | |
| 406 | |
| 407 **Closed issues:** | |
| 408 | |
| 409 - Roary not checking tools needed to run [\#214](https://github.com/sanger-pathogens/Roary/issues/214) | |
| 410 | |
| 411 **Merged pull requests:** | |
| 412 | |
| 413 - Core gene count [\#213](https://github.com/sanger-pathogens/Roary/pull/213) ([andrewjpage](https://github.com/andrewjpage)) | |
| 414 | |
| 415 ## [v3.5.6](https://github.com/sanger-pathogens/Roary/tree/v3.5.6) (2015-12-01) | |
| 416 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.5...v3.5.6) | |
| 417 | |
| 418 **Implemented enhancements:** | |
| 419 | |
| 420 - Non-issue, FYI regarding my 'roary2svg.pl' script [\#195](https://github.com/sanger-pathogens/Roary/issues/195) | |
| 421 | |
| 422 **Merged pull requests:** | |
| 423 | |
| 424 - add roary2svg script [\#212](https://github.com/sanger-pathogens/Roary/pull/212) ([andrewjpage](https://github.com/andrewjpage)) | |
| 425 | |
| 426 ## [v3.5.5](https://github.com/sanger-pathogens/Roary/tree/v3.5.5) (2015-11-26) | |
| 427 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.4...v3.5.5) | |
| 428 | |
| 429 **Merged pull requests:** | |
| 430 | |
| 431 - CD-hit threads limit [\#211](https://github.com/sanger-pathogens/Roary/pull/211) ([andrewjpage](https://github.com/andrewjpage)) | |
| 432 | |
| 433 ## [v3.5.4](https://github.com/sanger-pathogens/Roary/tree/v3.5.4) (2015-11-26) | |
| 434 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.3...v3.5.4) | |
| 435 | |
| 436 **Fixed bugs:** | |
| 437 | |
| 438 - Use of uninitialized value in require at \(eval ..\) line 1. [\#204](https://github.com/sanger-pathogens/Roary/issues/204) | |
| 439 - \[bug\] Newick files in 3.5.1 have branch lengths of 0.0 [\#202](https://github.com/sanger-pathogens/Roary/issues/202) | |
| 440 | |
| 441 **Merged pull requests:** | |
| 442 | |
| 443 - Accessory binary fasta contains all C's fix [\#210](https://github.com/sanger-pathogens/Roary/pull/210) ([andrewjpage](https://github.com/andrewjpage)) | |
| 444 | |
| 445 ## [v3.5.3](https://github.com/sanger-pathogens/Roary/tree/v3.5.3) (2015-11-26) | |
| 446 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.2...v3.5.3) | |
| 447 | |
| 448 **Implemented enhancements:** | |
| 449 | |
| 450 - Enhancement: roary -a to continue on if other parameters as well [\#207](https://github.com/sanger-pathogens/Roary/issues/207) | |
| 451 - Make summary\_statistics a TAB/TSV file? [\#193](https://github.com/sanger-pathogens/Roary/issues/193) | |
| 452 | |
| 453 **Fixed bugs:** | |
| 454 | |
| 455 - roary --version should return 0 not 255 exit code [\#206](https://github.com/sanger-pathogens/Roary/issues/206) | |
| 456 - Is the roary -a check complete? [\#205](https://github.com/sanger-pathogens/Roary/issues/205) | |
| 457 | |
| 458 ## [v3.5.2](https://github.com/sanger-pathogens/Roary/tree/v3.5.2) (2015-11-25) | |
| 459 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.1...v3.5.2) | |
| 460 | |
| 461 **Fixed bugs:** | |
| 462 | |
| 463 - Use of uninitialized value in File::Slurper and Encode.pm [\#196](https://github.com/sanger-pathogens/Roary/issues/196) | |
| 464 | |
| 465 **Merged pull requests:** | |
| 466 | |
| 467 - Improved dependancy checking [\#209](https://github.com/sanger-pathogens/Roary/pull/209) ([andrewjpage](https://github.com/andrewjpage)) | |
| 468 - Lsf update gene alignments [\#201](https://github.com/sanger-pathogens/Roary/pull/201) ([andrewjpage](https://github.com/andrewjpage)) | |
| 469 | |
| 470 ## [v3.5.1](https://github.com/sanger-pathogens/Roary/tree/v3.5.1) (2015-11-12) | |
| 471 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.0...v3.5.1) | |
| 472 | |
| 473 **Fixed bugs:** | |
| 474 | |
| 475 - Accessory genes newick file contains full path of infividual files [\#200](https://github.com/sanger-pathogens/Roary/issues/200) | |
| 476 - add optional dependancy from File::Slurper to stop warnings being printed [\#199](https://github.com/sanger-pathogens/Roary/pull/199) ([andrewjpage](https://github.com/andrewjpage)) | |
| 477 | |
| 478 ## [v3.5.0](https://github.com/sanger-pathogens/Roary/tree/v3.5.0) (2015-11-12) | |
| 479 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.3...v3.5.0) | |
| 480 | |
| 481 **Merged pull requests:** | |
| 482 | |
| 483 - remove path from accessory tree [\#198](https://github.com/sanger-pathogens/Roary/pull/198) ([andrewjpage](https://github.com/andrewjpage)) | |
| 484 | |
| 485 ## [v3.4.3](https://github.com/sanger-pathogens/Roary/tree/v3.4.3) (2015-11-11) | |
| 486 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.2...v3.4.3) | |
| 487 | |
| 488 **Merged pull requests:** | |
| 489 | |
| 490 - consensus group name for pan reference [\#190](https://github.com/sanger-pathogens/Roary/pull/190) ([andrewjpage](https://github.com/andrewjpage)) | |
| 491 | |
| 492 ## [v3.4.2](https://github.com/sanger-pathogens/Roary/tree/v3.4.2) (2015-10-12) | |
| 493 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.1...v3.4.2) | |
| 494 | |
| 495 **Merged pull requests:** | |
| 496 | |
| 497 - Gene presence and absence rtab [\#189](https://github.com/sanger-pathogens/Roary/pull/189) ([andrewjpage](https://github.com/andrewjpage)) | |
| 498 | |
| 499 ## [v3.4.1](https://github.com/sanger-pathogens/Roary/tree/v3.4.1) (2015-10-08) | |
| 500 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.0...v3.4.1) | |
| 501 | |
| 502 **Implemented enhancements:** | |
| 503 | |
| 504 - Need protein lengths in the final spreadsheet [\#116](https://github.com/sanger-pathogens/Roary/issues/116) | |
| 505 | |
| 506 **Fixed bugs:** | |
| 507 | |
| 508 - Bio-RetrieveAssemblies-1.0.1 fails to install [\#151](https://github.com/sanger-pathogens/Roary/issues/151) | |
| 509 | |
| 510 **Merged pull requests:** | |
| 511 | |
| 512 - \* Proposed fix for CPANTS error. [\#187](https://github.com/sanger-pathogens/Roary/pull/187) ([manwar](https://github.com/manwar)) | |
| 513 | |
| 514 ## [v3.4.0](https://github.com/sanger-pathogens/Roary/tree/v3.4.0) (2015-10-07) | |
| 515 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.4...v3.4.0) | |
| 516 | |
| 517 **Merged pull requests:** | |
| 518 | |
| 519 - Extra columns in spreadsheet with gene lengths [\#186](https://github.com/sanger-pathogens/Roary/pull/186) ([andrewjpage](https://github.com/andrewjpage)) | |
| 520 | |
| 521 ## [v3.3.4](https://github.com/sanger-pathogens/Roary/tree/v3.3.4) (2015-10-07) | |
| 522 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.3...v3.3.4) | |
| 523 | |
| 524 **Closed issues:** | |
| 525 | |
| 526 - EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa [\#175](https://github.com/sanger-pathogens/Roary/issues/175) | |
| 527 | |
| 528 **Merged pull requests:** | |
| 529 | |
| 530 - increase dependancy RAM [\#185](https://github.com/sanger-pathogens/Roary/pull/185) ([andrewjpage](https://github.com/andrewjpage)) | |
| 531 - Use lsf for gene alignment [\#184](https://github.com/sanger-pathogens/Roary/pull/184) ([andrewjpage](https://github.com/andrewjpage)) | |
| 532 | |
| 533 ## [v3.3.3](https://github.com/sanger-pathogens/Roary/tree/v3.3.3) (2015-09-29) | |
| 534 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.2...v3.3.3) | |
| 535 | |
| 536 **Merged pull requests:** | |
| 537 | |
| 538 - dont align if sequences same length and nearly the same [\#183](https://github.com/sanger-pathogens/Roary/pull/183) ([andrewjpage](https://github.com/andrewjpage)) | |
| 539 | |
| 540 ## [v3.3.2](https://github.com/sanger-pathogens/Roary/tree/v3.3.2) (2015-09-28) | |
| 541 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.1...v3.3.2) | |
| 542 | |
| 543 **Implemented enhancements:** | |
| 544 | |
| 545 - Use of temporary folders and files [\#177](https://github.com/sanger-pathogens/Roary/issues/177) | |
| 546 | |
| 547 **Merged pull requests:** | |
| 548 | |
| 549 - Duplicate sequences in pan genome reference fasta [\#182](https://github.com/sanger-pathogens/Roary/pull/182) ([andrewjpage](https://github.com/andrewjpage)) | |
| 550 | |
| 551 ## [v3.3.1](https://github.com/sanger-pathogens/Roary/tree/v3.3.1) (2015-09-25) | |
| 552 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.0...v3.3.1) | |
| 553 | |
| 554 **Merged pull requests:** | |
| 555 | |
| 556 - Fix usage text [\#181](https://github.com/sanger-pathogens/Roary/pull/181) ([andrewjpage](https://github.com/andrewjpage)) | |
| 557 | |
| 558 ## [v3.3.0](https://github.com/sanger-pathogens/Roary/tree/v3.3.0) (2015-09-24) | |
| 559 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.9...v3.3.0) | |
| 560 | |
| 561 **Fixed bugs:** | |
| 562 | |
| 563 - Check at least 2 gff files have been passed in [\#171](https://github.com/sanger-pathogens/Roary/issues/171) | |
| 564 - Pentuple memory for worst case sCenario [\#170](https://github.com/sanger-pathogens/Roary/issues/170) | |
| 565 - 00\_requires\_external.t missing "mafft" ? [\#168](https://github.com/sanger-pathogens/Roary/issues/168) | |
| 566 | |
| 567 **Merged pull requests:** | |
| 568 | |
| 569 - Check dependancies [\#180](https://github.com/sanger-pathogens/Roary/pull/180) ([andrewjpage](https://github.com/andrewjpage)) | |
| 570 | |
| 571 ## [v3.2.9](https://github.com/sanger-pathogens/Roary/tree/v3.2.9) (2015-09-23) | |
| 572 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.8...v3.2.9) | |
| 573 | |
| 574 **Implemented enhancements:** | |
| 575 | |
| 576 - Add --outdir option to avoid blatting current directory [\#176](https://github.com/sanger-pathogens/Roary/issues/176) | |
| 577 | |
| 578 **Fixed bugs:** | |
| 579 | |
| 580 - CPAN install failure "unknown option mafft" [\#169](https://github.com/sanger-pathogens/Roary/issues/169) | |
| 581 | |
| 582 **Closed issues:** | |
| 583 | |
| 584 - Error "Cant open file: \_uninflated\_mcl\_groups" [\#179](https://github.com/sanger-pathogens/Roary/issues/179) | |
| 585 | |
| 586 **Merged pull requests:** | |
| 587 | |
| 588 - Add the option to specify an output directory [\#178](https://github.com/sanger-pathogens/Roary/pull/178) ([andrewjpage](https://github.com/andrewjpage)) | |
| 589 | |
| 590 ## [v3.2.8](https://github.com/sanger-pathogens/Roary/tree/v3.2.8) (2015-09-23) | |
| 591 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.7...v3.2.8) | |
| 592 | |
| 593 ## [v3.2.7](https://github.com/sanger-pathogens/Roary/tree/v3.2.7) (2015-09-02) | |
| 594 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.6...v3.2.7) | |
| 595 | |
| 596 **Merged pull requests:** | |
| 597 | |
| 598 - count paralogs correctly when looking for differences in datasets [\#174](https://github.com/sanger-pathogens/Roary/pull/174) ([andrewjpage](https://github.com/andrewjpage)) | |
| 599 | |
| 600 ## [v3.2.6](https://github.com/sanger-pathogens/Roary/tree/v3.2.6) (2015-09-02) | |
| 601 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.5...v3.2.6) | |
| 602 | |
| 603 **Merged pull requests:** | |
| 604 | |
| 605 - revert core tree generation [\#173](https://github.com/sanger-pathogens/Roary/pull/173) ([andrewjpage](https://github.com/andrewjpage)) | |
| 606 | |
| 607 ## [v3.2.5](https://github.com/sanger-pathogens/Roary/tree/v3.2.5) (2015-08-17) | |
| 608 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.4...v3.2.5) | |
| 609 | |
| 610 **Merged pull requests:** | |
| 611 | |
| 612 - Verbose stats [\#172](https://github.com/sanger-pathogens/Roary/pull/172) ([andrewjpage](https://github.com/andrewjpage)) | |
| 613 - dont set bioperl version [\#167](https://github.com/sanger-pathogens/Roary/pull/167) ([andrewjpage](https://github.com/andrewjpage)) | |
| 614 | |
| 615 ## [v3.2.4](https://github.com/sanger-pathogens/Roary/tree/v3.2.4) (2015-07-23) | |
| 616 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.3...v3.2.4) | |
| 617 | |
| 618 **Merged pull requests:** | |
| 619 | |
| 620 - update readme citation [\#165](https://github.com/sanger-pathogens/Roary/pull/165) ([andrewjpage](https://github.com/andrewjpage)) | |
| 621 | |
| 622 ## [v3.2.3](https://github.com/sanger-pathogens/Roary/tree/v3.2.3) (2015-07-22) | |
| 623 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.1...v3.2.3) | |
| 624 | |
| 625 **Merged pull requests:** | |
| 626 | |
| 627 - update citation message [\#164](https://github.com/sanger-pathogens/Roary/pull/164) ([andrewjpage](https://github.com/andrewjpage)) | |
| 628 - Pass mafft through to alignment [\#163](https://github.com/sanger-pathogens/Roary/pull/163) ([andrewjpage](https://github.com/andrewjpage)) | |
| 629 | |
| 630 ## [v3.2.1](https://github.com/sanger-pathogens/Roary/tree/v3.2.1) (2015-07-21) | |
| 631 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.0...v3.2.1) | |
| 632 | |
| 633 ## [v3.2.0](https://github.com/sanger-pathogens/Roary/tree/v3.2.0) (2015-07-20) | |
| 634 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.2...v3.2.0) | |
| 635 | |
| 636 **Merged pull requests:** | |
| 637 | |
| 638 - Use mafft [\#162](https://github.com/sanger-pathogens/Roary/pull/162) ([andrewjpage](https://github.com/andrewjpage)) | |
| 639 - output summary file [\#161](https://github.com/sanger-pathogens/Roary/pull/161) ([andrewjpage](https://github.com/andrewjpage)) | |
| 640 - Pass through dont delete flag [\#160](https://github.com/sanger-pathogens/Roary/pull/160) ([andrewjpage](https://github.com/andrewjpage)) | |
| 641 - Assembly statistics [\#159](https://github.com/sanger-pathogens/Roary/pull/159) ([andrewjpage](https://github.com/andrewjpage)) | |
| 642 | |
| 643 ## [v3.1.2](https://github.com/sanger-pathogens/Roary/tree/v3.1.2) (2015-07-13) | |
| 644 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/3.1.2...v3.1.2) | |
| 645 | |
| 646 ## [3.1.2](https://github.com/sanger-pathogens/Roary/tree/3.1.2) (2015-07-13) | |
| 647 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.1...3.1.2) | |
| 648 | |
| 649 **Fixed bugs:** | |
| 650 | |
| 651 - prank seg fault [\#157](https://github.com/sanger-pathogens/Roary/issues/157) | |
| 652 | |
| 653 **Merged pull requests:** | |
| 654 | |
| 655 - Core gene missing files [\#158](https://github.com/sanger-pathogens/Roary/pull/158) ([andrewjpage](https://github.com/andrewjpage)) | |
| 656 | |
| 657 ## [v3.1.1](https://github.com/sanger-pathogens/Roary/tree/v3.1.1) (2015-06-26) | |
| 658 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.0...v3.1.1) | |
| 659 | |
| 660 **Closed issues:** | |
| 661 | |
| 662 - sadaf [\#154](https://github.com/sanger-pathogens/Roary/issues/154) | |
| 663 | |
| 664 ## [v3.1.0](https://github.com/sanger-pathogens/Roary/tree/v3.1.0) (2015-06-22) | |
| 665 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.3...v3.1.0) | |
| 666 | |
| 667 **Merged pull requests:** | |
| 668 | |
| 669 - Accessory binary tree [\#155](https://github.com/sanger-pathogens/Roary/pull/155) ([andrewjpage](https://github.com/andrewjpage)) | |
| 670 | |
| 671 ## [v3.0.3](https://github.com/sanger-pathogens/Roary/tree/v3.0.3) (2015-06-15) | |
| 672 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.2...v3.0.3) | |
| 673 | |
| 674 **Fixed bugs:** | |
| 675 | |
| 676 - Annotation missing in set\_difference\_unique\_set\_one/two\_statistics.csv files [\#137](https://github.com/sanger-pathogens/Roary/issues/137) | |
| 677 | |
| 678 **Merged pull requests:** | |
| 679 | |
| 680 - when creating core gene alignment, lookup sample names to genes in sp… [\#153](https://github.com/sanger-pathogens/Roary/pull/153) ([andrewjpage](https://github.com/andrewjpage)) | |
| 681 - Only align core files [\#150](https://github.com/sanger-pathogens/Roary/pull/150) ([andrewjpage](https://github.com/andrewjpage)) | |
| 682 | |
| 683 ## [v3.0.2](https://github.com/sanger-pathogens/Roary/tree/v3.0.2) (2015-06-12) | |
| 684 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.1...v3.0.2) | |
| 685 | |
| 686 **Implemented enhancements:** | |
| 687 | |
| 688 - Print out the version number [\#119](https://github.com/sanger-pathogens/Roary/issues/119) | |
| 689 | |
| 690 **Merged pull requests:** | |
| 691 | |
| 692 - Mafft and exonerate dependancies [\#149](https://github.com/sanger-pathogens/Roary/pull/149) ([andrewjpage](https://github.com/andrewjpage)) | |
| 693 - Add a version parameter and add in marcos plots code [\#148](https://github.com/sanger-pathogens/Roary/pull/148) ([andrewjpage](https://github.com/andrewjpage)) | |
| 694 | |
| 695 ## [v3.0.1](https://github.com/sanger-pathogens/Roary/tree/v3.0.1) (2015-06-12) | |
| 696 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.0...v3.0.1) | |
| 697 | |
| 698 **Fixed bugs:** | |
| 699 | |
| 700 - Use of -e switch gives multifasta file with N's only [\#132](https://github.com/sanger-pathogens/Roary/issues/132) | |
| 701 | |
| 702 ## [v3.0.0](https://github.com/sanger-pathogens/Roary/tree/v3.0.0) (2015-06-11) | |
| 703 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.4...v3.0.0) | |
| 704 | |
| 705 **Merged pull requests:** | |
| 706 | |
| 707 - Use prank for core genome alignments [\#147](https://github.com/sanger-pathogens/Roary/pull/147) ([andrewjpage](https://github.com/andrewjpage)) | |
| 708 - Accessory graph [\#146](https://github.com/sanger-pathogens/Roary/pull/146) ([andrewjpage](https://github.com/andrewjpage)) | |
| 709 | |
| 710 ## [v2.3.4](https://github.com/sanger-pathogens/Roary/tree/v2.3.4) (2015-06-10) | |
| 711 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.3...v2.3.4) | |
| 712 | |
| 713 ## [v2.3.3](https://github.com/sanger-pathogens/Roary/tree/v2.3.3) (2015-06-08) | |
| 714 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.2...v2.3.3) | |
| 715 | |
| 716 **Merged pull requests:** | |
| 717 | |
| 718 - Simplify perl dependency installation [\#145](https://github.com/sanger-pathogens/Roary/pull/145) ([bewt85](https://github.com/bewt85)) | |
| 719 - Pan genome reference [\#144](https://github.com/sanger-pathogens/Roary/pull/144) ([andrewjpage](https://github.com/andrewjpage)) | |
| 720 - Fix input files with duplicate IDs [\#143](https://github.com/sanger-pathogens/Roary/pull/143) ([andrewjpage](https://github.com/andrewjpage)) | |
| 721 - Test against different versions of GNU Parallel [\#142](https://github.com/sanger-pathogens/Roary/pull/142) ([bewt85](https://github.com/bewt85)) | |
| 722 | |
| 723 ## [v2.3.2](https://github.com/sanger-pathogens/Roary/tree/v2.3.2) (2015-06-08) | |
| 724 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.1...v2.3.2) | |
| 725 | |
| 726 **Fixed bugs:** | |
| 727 | |
| 728 - GFF files derived from Prokka genbank raise errors [\#130](https://github.com/sanger-pathogens/Roary/issues/130) | |
| 729 - MSG: Got a sequence without letters. Could not guess alphabet [\#127](https://github.com/sanger-pathogens/Roary/issues/127) | |
| 730 | |
| 731 **Merged pull requests:** | |
| 732 | |
| 733 - TravisCI only wants the major and minor version of perl [\#141](https://github.com/sanger-pathogens/Roary/pull/141) ([bewt85](https://github.com/bewt85)) | |
| 734 - Add TravisCI support [\#140](https://github.com/sanger-pathogens/Roary/pull/140) ([bewt85](https://github.com/bewt85)) | |
| 735 - Use locus tag when ID is missing from GFF [\#139](https://github.com/sanger-pathogens/Roary/pull/139) ([andrewjpage](https://github.com/andrewjpage)) | |
| 736 | |
| 737 ## [v2.3.1](https://github.com/sanger-pathogens/Roary/tree/v2.3.1) (2015-06-02) | |
| 738 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.0...v2.3.1) | |
| 739 | |
| 740 **Merged pull requests:** | |
| 741 | |
| 742 - Extract IDs from GFF file using Bio::Perl [\#138](https://github.com/sanger-pathogens/Roary/pull/138) ([andrewjpage](https://github.com/andrewjpage)) | |
| 743 | |
| 744 ## [v2.3.0](https://github.com/sanger-pathogens/Roary/tree/v2.3.0) (2015-06-01) | |
| 745 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.6...v2.3.0) | |
| 746 | |
| 747 **Closed issues:** | |
| 748 | |
| 749 - "cpan" command reports Bio::Roary as version '\(undef\)' [\#134](https://github.com/sanger-pathogens/Roary/issues/134) | |
| 750 | |
| 751 ## [v2.2.6](https://github.com/sanger-pathogens/Roary/tree/v2.2.6) (2015-06-01) | |
| 752 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.4...v2.2.6) | |
| 753 | |
| 754 **Closed issues:** | |
| 755 | |
| 756 - No tagged release for 2.2.3 [\#133](https://github.com/sanger-pathogens/Roary/issues/133) | |
| 757 - Syntax \(?\) errors on perl 5.10.1 [\#128](https://github.com/sanger-pathogens/Roary/issues/128) | |
| 758 | |
| 759 **Merged pull requests:** | |
| 760 | |
| 761 - include version numbers for cpan [\#136](https://github.com/sanger-pathogens/Roary/pull/136) ([andrewjpage](https://github.com/andrewjpage)) | |
| 762 - New version number for contributed fix for issue \#128 [\#135](https://github.com/sanger-pathogens/Roary/pull/135) ([andrewjpage](https://github.com/andrewjpage)) | |
| 763 - gnu parallel switch for ubuntu [\#131](https://github.com/sanger-pathogens/Roary/pull/131) ([andrewjpage](https://github.com/andrewjpage)) | |
| 764 - Backward compatible deferencing of hashes [\#129](https://github.com/sanger-pathogens/Roary/pull/129) ([mgalardini](https://github.com/mgalardini)) | |
| 765 | |
| 766 ## [v2.2.4](https://github.com/sanger-pathogens/Roary/tree/v2.2.4) (2015-05-29) | |
| 767 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.3...v2.2.4) | |
| 768 | |
| 769 **Closed issues:** | |
| 770 | |
| 771 - ERROR: cannot remove directory for split\_groups [\#115](https://github.com/sanger-pathogens/Roary/issues/115) | |
| 772 - cleanup outputfiles [\#114](https://github.com/sanger-pathogens/Roary/issues/114) | |
| 773 | |
| 774 **Merged pull requests:** | |
| 775 | |
| 776 - Cleanup files [\#126](https://github.com/sanger-pathogens/Roary/pull/126) ([andrewjpage](https://github.com/andrewjpage)) | |
| 777 | |
| 778 ## [v2.2.3](https://github.com/sanger-pathogens/Roary/tree/v2.2.3) (2015-05-21) | |
| 779 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.2...v2.2.3) | |
| 780 | |
| 781 **Closed issues:** | |
| 782 | |
| 783 - Change QC so that it doesnt shred reads [\#117](https://github.com/sanger-pathogens/Roary/issues/117) | |
| 784 - QC doesnt work outside sanger [\#112](https://github.com/sanger-pathogens/Roary/issues/112) | |
| 785 | |
| 786 **Merged pull requests:** | |
| 787 | |
| 788 - Update Kraken QC [\#125](https://github.com/sanger-pathogens/Roary/pull/125) ([andrewjpage](https://github.com/andrewjpage)) | |
| 789 | |
| 790 ## [v2.2.2](https://github.com/sanger-pathogens/Roary/tree/v2.2.2) (2015-05-21) | |
| 791 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.0...v2.2.2) | |
| 792 | |
| 793 **Closed issues:** | |
| 794 | |
| 795 - Hard-coded Sanger paths in some scripts [\#124](https://github.com/sanger-pathogens/Roary/issues/124) | |
| 796 - You're missing some Perl dependancies [\#123](https://github.com/sanger-pathogens/Roary/issues/123) | |
| 797 - Add support for GFF files from NCBI [\#120](https://github.com/sanger-pathogens/Roary/issues/120) | |
| 798 | |
| 799 **Merged pull requests:** | |
| 800 | |
| 801 - Fix usage text [\#122](https://github.com/sanger-pathogens/Roary/pull/122) ([andrewjpage](https://github.com/andrewjpage)) | |
| 802 | |
| 803 ## [v2.2.0](https://github.com/sanger-pathogens/Roary/tree/v2.2.0) (2015-05-14) | |
| 804 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.2...v2.2.0) | |
| 805 | |
| 806 **Closed issues:** | |
| 807 | |
| 808 - Verbose output with -v [\#113](https://github.com/sanger-pathogens/Roary/issues/113) | |
| 809 | |
| 810 **Merged pull requests:** | |
| 811 | |
| 812 - Accept genbank files [\#121](https://github.com/sanger-pathogens/Roary/pull/121) ([andrewjpage](https://github.com/andrewjpage)) | |
| 813 | |
| 814 ## [v2.1.2](https://github.com/sanger-pathogens/Roary/tree/v2.1.2) (2015-05-12) | |
| 815 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.1...v2.1.2) | |
| 816 | |
| 817 **Merged pull requests:** | |
| 818 | |
| 819 - Verbose output [\#118](https://github.com/sanger-pathogens/Roary/pull/118) ([andrewjpage](https://github.com/andrewjpage)) | |
| 820 | |
| 821 ## [v2.1.1](https://github.com/sanger-pathogens/Roary/tree/v2.1.1) (2015-04-29) | |
| 822 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.9...v2.1.1) | |
| 823 | |
| 824 **Merged pull requests:** | |
| 825 | |
| 826 - pass core definition into number of conserved genes plot [\#111](https://github.com/sanger-pathogens/Roary/pull/111) ([andrewjpage](https://github.com/andrewjpage)) | |
| 827 - Vary core definition [\#110](https://github.com/sanger-pathogens/Roary/pull/110) ([andrewjpage](https://github.com/andrewjpage)) | |
| 828 - Use block quotes in readme [\#109](https://github.com/sanger-pathogens/Roary/pull/109) ([bewt85](https://github.com/bewt85)) | |
| 829 | |
| 830 ## [v2.0.9](https://github.com/sanger-pathogens/Roary/tree/v2.0.9) (2015-04-20) | |
| 831 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.8...v2.0.9) | |
| 832 | |
| 833 **Merged pull requests:** | |
| 834 | |
| 835 - Allow for multiple processors to be used [\#108](https://github.com/sanger-pathogens/Roary/pull/108) ([andrewjpage](https://github.com/andrewjpage)) | |
| 836 | |
| 837 ## [v2.0.8](https://github.com/sanger-pathogens/Roary/tree/v2.0.8) (2015-04-09) | |
| 838 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.7...v2.0.8) | |
| 839 | |
| 840 **Merged pull requests:** | |
| 841 | |
| 842 - Speedup [\#107](https://github.com/sanger-pathogens/Roary/pull/107) ([andrewjpage](https://github.com/andrewjpage)) | |
| 843 - new version 2.0.7 [\#106](https://github.com/sanger-pathogens/Roary/pull/106) ([andrewjpage](https://github.com/andrewjpage)) | |
| 844 | |
| 845 ## [v2.0.7](https://github.com/sanger-pathogens/Roary/tree/v2.0.7) (2015-03-28) | |
| 846 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.5...v2.0.7) | |
| 847 | |
| 848 **Merged pull requests:** | |
| 849 | |
| 850 - old splits [\#105](https://github.com/sanger-pathogens/Roary/pull/105) ([andrewjpage](https://github.com/andrewjpage)) | |
| 851 - Speedup split [\#104](https://github.com/sanger-pathogens/Roary/pull/104) ([andrewjpage](https://github.com/andrewjpage)) | |
| 852 | |
| 853 ## [v2.0.5](https://github.com/sanger-pathogens/Roary/tree/v2.0.5) (2015-03-26) | |
| 854 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.4...v2.0.5) | |
| 855 | |
| 856 **Merged pull requests:** | |
| 857 | |
| 858 - Stop deep recursion [\#103](https://github.com/sanger-pathogens/Roary/pull/103) ([andrewjpage](https://github.com/andrewjpage)) | |
| 859 - check programs installed [\#102](https://github.com/sanger-pathogens/Roary/pull/102) ([andrewjpage](https://github.com/andrewjpage)) | |
| 860 | |
| 861 ## [2.0.4](https://github.com/sanger-pathogens/Roary/tree/2.0.4) (2015-03-23) | |
| 862 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4) | |
| 863 | |
| 864 **Merged pull requests:** | |
| 865 | |
| 866 - File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage)) | |
| 867 - version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage)) | |
| 868 | |
| 869 ## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17) | |
| 870 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3) | |
| 871 | |
| 872 **Merged pull requests:** | |
| 873 | |
| 874 - Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage)) | |
| 875 - Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage)) | |
| 876 - Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage)) | |
| 877 | |
| 878 ## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16) | |
| 879 **Merged pull requests:** | |
| 880 | |
| 881 - Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage)) | |
| 882 - Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins)) | |
| 883 - Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage)) | |
| 884 - Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage)) | |
| 885 - rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage)) | |
| 886 - Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage)) | |
| 887 - remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage)) | |
| 888 - Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage)) | |
| 889 - Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins)) | |
| 890 - QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins)) | |
| 891 - increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage)) | |
| 892 - Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage)) | |
| 893 - 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)) | |
| 894 - Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins)) | |
| 895 - Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins)) | |
| 896 - Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins)) | |
| 897 - Multifastas not created when group limit \(default 8000\) exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins)) | |
| 898 - allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage)) | |
| 899 - increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage)) | |
| 900 - Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage)) | |
| 901 - Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins)) | |
| 902 - Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1)) | |
| 903 - 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)) | |
| 904 - use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage)) | |
| 905 - core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage)) | |
| 906 - Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage)) | |
| 907 - Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage)) | |
| 908 - Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage)) | |
| 909 - update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage)) | |
| 910 - Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage)) | |
| 911 - make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage)) | |
| 912 - script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage)) | |
| 913 - rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage)) | |
| 914 - Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage)) | |
| 915 - Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage)) | |
| 916 - make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage)) | |
| 917 - query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage)) | |
| 918 - fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage)) | |
| 919 - Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage)) | |
| 920 - add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage)) | |
| 921 - 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)) | |
| 922 - print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage)) | |
| 923 - Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage)) | |
| 924 - fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage)) | |
| 925 - Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage)) | |
| 926 - Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage)) | |
| 927 - pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage)) | |
| 928 - iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage)) | |
| 929 - Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage)) | |
| 930 - Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage)) | |
| 931 - dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage)) | |
| 932 - rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage)) | |
| 933 - cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage)) | |
| 934 - Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage)) | |
| 935 - align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage)) | |
| 936 - Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage)) | |
| 937 - Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage)) | |
| 938 - Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage)) | |
| 939 - Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage)) | |
| 940 - split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage)) | |
| 941 - make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage)) | |
| 942 - dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage)) | |
| 943 - run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage)) | |
| 944 - annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage)) | |
| 945 - Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage)) | |
| 946 - Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage)) | |
| 947 - remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage)) | |
| 948 - blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage)) | |
| 949 - Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage)) | |
| 950 - Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage)) | |
| 951 - Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage)) | |
| 952 - use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage)) | |
| 953 - renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter)) | |
| 954 - GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage)) | |
| 955 - lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage)) | |
| 956 - low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage)) | |
| 957 - inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage)) | |
| 958 - report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage)) | |
| 959 - update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage)) | |
| 960 - speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage)) | |
| 961 - sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage)) | |
| 962 - create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage)) | |
| 963 - Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage)) | |
| 964 - Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage)) | |
| 965 - check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage)) | |
| 966 - catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage)) | |
| 967 - tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage)) | |
| 968 - label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage)) | |
| 969 - 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)) | |
| 970 - transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage)) | |
| 971 - speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage)) | |
| 972 - typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage)) | |
| 973 - run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage)) | |
| 974 - vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage)) | |
| 975 - working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage)) | |
| 976 - Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage)) | |
| 977 |