| 0ddeec7 | Keiran Raine | 20 July 2015, 09:37:22 UTC | Merge branch 'hotfix/v2.1.2' | 20 July 2015, 09:37:22 UTC |
| c494dd6 | Keiran Raine | 20 July 2015, 08:46:53 UTC | doc cleanup | 20 July 2015, 08:46:53 UTC |
| 9c88b84 | Keiran Raine | 20 July 2015, 08:35:15 UTC | Merge branch 'hotfix/v2.1.1' | 20 July 2015, 08:35:15 UTC |
| 9bee6ed | Keiran Raine | 20 July 2015, 08:34:48 UTC | Fixed missing capture of '-q' param and updated licence dates | 20 July 2015, 08:34:48 UTC |
| af652d4 | David Jones | 14 April 2015, 09:22:59 UTC | Merge branch 'release/2.1.0' | 14 April 2015, 09:22:59 UTC |
| f651d22 | David Jones | 14 April 2015, 09:21:51 UTC | Ran prerelease, checked install with patch for c htslib | 14 April 2015, 09:21:51 UTC |
| 706cfd3 | Keiran Raine | 14 April 2015, 08:33:34 UTC | Merge pull request #16 from cancerit/dev Patch for htslib, added version to alleleCounter C, fixed allelecounter c region malloc | 14 April 2015, 08:33:34 UTC |
| a4817c7 | David Jones | 13 April 2015, 10:28:40 UTC | Added patch to htslib for carm index as it's currently unreleased | 13 April 2015, 10:28:40 UTC |
| 8035c7e | David Jones | 13 April 2015, 09:12:16 UTC | Ran prerelease.sh | 13 April 2015, 09:12:16 UTC |
| e2d596c | David Jones | 13 April 2015, 09:10:29 UTC | Update CHANGES.md | 13 April 2015, 09:10:29 UTC |
| 60e7985 | David Jones | 13 April 2015, 09:08:38 UTC | Merge branch 'dev' of https://github.com/cancerit/alleleCount into dev | 13 April 2015, 09:08:38 UTC |
| ff013db | David Jones | 13 April 2015, 09:08:27 UTC | Added CHANGES.md | 13 April 2015, 09:08:27 UTC |
| 3ba489a | David Jones | 13 April 2015, 09:06:46 UTC | Update README.md | 13 April 2015, 09:06:46 UTC |
| b6c8ebc | David Jones | 13 April 2015, 09:02:56 UTC | Bumped perl version | 13 April 2015, 09:02:56 UTC |
| 8e10940 | David Jones | 13 April 2015, 09:01:59 UTC | Bug fix to region malloc in bam_access. Added version information. Makefile will need updating on each iteration of version. | 13 April 2015, 09:01:59 UTC |
| 2687199 | David Jones | 06 March 2015, 16:17:17 UTC | Merge pull request #13 from cancerit/dev Updates for version 2.0.1 | 06 March 2015, 16:17:17 UTC |
| 808443c | David Jones | 06 March 2015, 16:16:52 UTC | prerelease info updated for release 2.0.1 | 06 March 2015, 16:16:52 UTC |
| ead6184 | David Jones | 06 March 2015, 13:59:01 UTC | updated for release 2.0.1 | 06 March 2015, 13:59:01 UTC |
| ba18bfd | David Jones | 06 March 2015, 13:57:18 UTC | Update AlleleCount.pm Changed version to a bugfix of 2.0 for release of alleleCounter c correction | 06 March 2015, 13:57:18 UTC |
| ada2868 | Keiran Raine | 06 March 2015, 13:54:35 UTC | Merge pull request #12 from cancerit/dev Removed reference as a required param | 06 March 2015, 13:54:35 UTC |
| 10a5a72 | David Jones | 06 March 2015, 13:51:07 UTC | Merging alleleCount.c | 06 March 2015, 13:51:07 UTC |
| 3cf7b1d | David Jones | 06 March 2015, 13:40:04 UTC | reference no longer a required option. A warning is given at help, and if cram is supplied without reference as htslib may fail to find the reference listed in the cram header. | 06 March 2015, 13:40:04 UTC |
| e7065fc | Keiran Raine | 23 February 2015, 11:09:25 UTC | Merge pull request #11 from cancerit/dev Fixed up setup script and bumped version to 2.0.0 | 23 February 2015, 11:09:25 UTC |
| 4d4d459 | Keiran Raine | 23 February 2015, 11:04:17 UTC | Updated setup and related docs for CRAM addition to C code | 23 February 2015, 11:04:17 UTC |
| 8453e0f | David Jones | 23 February 2015, 10:41:43 UTC | Update -h information. Changed ref-file to say it needs a fasta index | 23 February 2015, 10:41:43 UTC |
| cc7d105 | David Jones | 20 February 2015, 16:49:29 UTC | Updated code to utilise htslib and removed requirement for samtools entirely. Now supports bam and cram inputs | 20 February 2015, 16:49:29 UTC |
| f06474b | David Jones | 20 February 2015, 16:45:25 UTC | Removed requirement for samtools and libbam. A few naming changes. Now converted to use htslib and work for both bam and cram | 20 February 2015, 16:45:25 UTC |
| e63a6fb | David Jones | 19 February 2015, 10:25:26 UTC | updated gitignore | 19 February 2015, 10:25:26 UTC |
| 905e285 | Keiran Raine | 08 October 2014, 13:26:26 UTC | Update README.md additional boiler plate should additional years be added | 08 October 2014, 13:26:26 UTC |
| ac8bb1c | Keiran Raine | 06 October 2014, 14:49:50 UTC | Merge pull request #8 from cancerit/master Sync with master | 06 October 2014, 14:49:50 UTC |
| 6c46028 | Keiran Raine | 06 October 2014, 14:47:30 UTC | Merge pull request #7 from cancerit/dev Updated to last stable samtools before htslib | 06 October 2014, 14:47:30 UTC |
| 39a5183 | Keiran Raine | 06 October 2014, 14:46:21 UTC | Updated to last stable samtools before htslib | 06 October 2014, 14:46:21 UTC |
| 0d61066 | AndyMenzies | 26 September 2014, 13:21:49 UTC | Merge pull request #6 from cancerit/dev fixed issue with availability of samtools header files for alleleCounter... | 26 September 2014, 13:21:49 UTC |
| 69ca8fc | Keiran Raine | 26 September 2014, 13:18:35 UTC | fixed issue with availability of samtools header files for alleleCounter compilation | 26 September 2014, 13:18:35 UTC |
| ddf41c6 | AndyMenzies | 26 September 2014, 08:31:11 UTC | Merge pull request #5 from cancerit/dev Fixed up the setup.sh script to install the C version of the code | 26 September 2014, 08:31:11 UTC |
| de04244 | Keiran Raine | 25 September 2014, 14:59:38 UTC | Fixed up the setup.sh script to install the C version of the code | 25 September 2014, 14:59:38 UTC |
| d7d946b | AndyMenzies | 03 September 2014, 12:16:59 UTC | Merge pull request #4 from cancerit/dev Pull C alleleCounter code and improvements to perl efficiency | 03 September 2014, 12:16:59 UTC |
| 7f798ab | David Jones | 02 September 2014, 09:58:49 UTC | Merge branch 'dev' of https://github.com/cancerit/alleleCount into dev | 02 September 2014, 09:58:49 UTC |
| 50e6ab0 | David Jones | 02 September 2014, 09:58:10 UTC | script for versioning and version changed 1.2.0 | 02 September 2014, 09:58:10 UTC |
| 6cf553a | David Jones | 28 August 2014, 10:13:22 UTC | Update to version 1.2.0 for release with C code | 28 August 2014, 10:13:22 UTC |
| 3851579 | David Jones | 15 August 2014, 08:19:41 UTC | Made memory allocation dynamic in region setting to allow for the size of genomes and larger numbers | 15 August 2014, 08:19:41 UTC |
| 4874a54 | David Jones | 15 August 2014, 08:14:22 UTC | Modified memory allocation to allow for the size of genomes and larger numbers | 15 August 2014, 08:14:22 UTC |
| 583e749 | David Jones | 15 August 2014, 08:06:33 UTC | Modified memory allocation to allow for the size of genomes and larger numbers | 15 August 2014, 08:06:33 UTC |
| 6d356bd | David Jones | 14 August 2014, 15:22:27 UTC | Fixed pileup->indel issue Changed to use the correct pileup->is_del | 14 August 2014, 15:22:27 UTC |
| a944b73 | David Jones | 08 August 2014, 14:35:48 UTC | Updated LICENSE | 08 August 2014, 14:35:48 UTC |
| 790b371 | David Jones | 08 August 2014, 14:35:28 UTC | Updated LICENSE | 08 August 2014, 14:35:28 UTC |
| f0695ee | David Jones | 07 August 2014, 15:29:21 UTC | Added test data for c testing purposes | 07 August 2014, 15:29:21 UTC |
| bc6b45c | David Jones | 07 August 2014, 15:28:39 UTC | Moved a couple of variable declarations to reduce warnings. Updated indel to is_del in stamtools pileup checks | 07 August 2014, 15:28:39 UTC |
| 739db21 | David Jones | 07 August 2014, 15:26:42 UTC | Tests added for bam_access | 07 August 2014, 15:26:42 UTC |
| bd2b5b7 | David Jones | 07 August 2014, 15:23:53 UTC | modified caveman target to counter target | 07 August 2014, 15:23:53 UTC |
| 05e8eb5 | David Jones | 29 July 2014, 12:20:22 UTC | c classes etc added. More efficient c implementation of allele counting | 29 July 2014, 12:20:22 UTC |
| c15cfc6 | David Jones | 29 July 2014, 12:19:52 UTC | Updated ignores to include c/bin | 29 July 2014, 12:19:52 UTC |
| db710ad | David Jones | 29 July 2014, 12:14:15 UTC | improvements to efficiency of perl code | 29 July 2014, 12:14:15 UTC |
| 688753a | AndyMenzies | 19 June 2014, 10:15:24 UTC | Merge pull request #3 from cancerit/dev Prep v.1.1.0 | 19 June 2014, 10:15:24 UTC |
| dcf6e55 | Keiran Raine | 19 June 2014, 10:12:29 UTC | prep 1.1.0 | 19 June 2014, 10:12:29 UTC |
| 36547da | AndyMenzies | 19 June 2014, 08:12:16 UTC | Merge pull request #2 from cancerit/1.0-pbq Separate out per-base-qual and mapping qual, also minor enhancement to P... | 19 June 2014, 08:12:16 UTC |
| ff9326b | Keiran Raine | 18 June 2014, 14:42:18 UTC | Remove 'InputFile' from header line | 18 June 2014, 14:42:18 UTC |
| 900c050 | Keiran Raine | 18 June 2014, 14:13:35 UTC | Remove filename from output, just makes a huge file | 18 June 2014, 14:13:35 UTC |
| 6a2875a | Keiran Raine | 18 June 2014, 13:26:10 UTC | Forgot to remove legacy comment | 18 June 2014, 13:26:10 UTC |
| e12d8b1 | Keiran Raine | 18 June 2014, 13:23:09 UTC | Separate out per-base-qual and mapping qual, also minor enhancement to PileupData->new | 18 June 2014, 13:23:09 UTC |
| b3f83e9 | Keiran Raine | 10 June 2014, 10:48:01 UTC | Merge pull request #1 from cancerit/dev Worked through changes with @AndyMenzies, looks good. | 10 June 2014, 10:48:01 UTC |
| 1a9feeb | Andy Menzies | 10 June 2014, 10:44:22 UTC | additions to MANIFEST.SKIP, reran prerelease | 10 June 2014, 10:44:22 UTC |
| 463ae2c | Andy Menzies | 10 June 2014, 10:39:20 UTC | updates from running prerelease script | 10 June 2014, 10:39:20 UTC |
| 7e7109f | Andy Menzies | 10 June 2014, 10:21:31 UTC | updating version number to 1.0.0 | 10 June 2014, 10:21:31 UTC |
| 288e71d | AndyMenzies | 10 June 2014, 10:02:59 UTC | fixing version number grab to look at correct class | 10 June 2014, 10:02:59 UTC |
| 6a9ec16 | AndyMenzies | 10 June 2014, 10:00:52 UTC | Correcting release instructions | 10 June 2014, 10:00:52 UTC |
| 62b5ace | Keiran Raine | 06 June 2014, 15:24:39 UTC | all cleaned up for push to GitHub | 06 June 2014, 15:24:39 UTC |
| d199c80 | Keiran Raine | 06 June 2014, 13:30:16 UTC | fix up prerelease script | 06 June 2014, 13:30:16 UTC |
| 1f8f2a6 | Keiran Raine | 06 June 2014, 13:25:37 UTC | Correcting structure so Makefile.PL will work | 06 June 2014, 13:25:37 UTC |
| 7c147a0 | Keiran Raine | 06 June 2014, 13:19:46 UTC | renamed README to markdown | 06 June 2014, 13:19:46 UTC |
| 6427243 | Keiran Raine | 06 June 2014, 13:19:26 UTC | cleanup licence and readme | 06 June 2014, 13:19:26 UTC |
| ef8df7e | Keiran Raine | 06 June 2014, 13:19:18 UTC | cleanup licence and readme | 06 June 2014, 13:19:18 UTC |
| 86bccbe | Andy Menzies | 06 June 2014, 13:07:22 UTC | more to ignore | 06 June 2014, 13:07:22 UTC |
| a8ced19 | Andy Menzies | 28 May 2014, 15:14:39 UTC | adding license to code | 28 May 2014, 15:14:39 UTC |
| 4aea122 | Andy Menzies | 22 May 2014, 11:00:38 UTC | initial check in of basic functional code. | 22 May 2014, 11:00:38 UTC |
