| 6da0438 | Lilian Janin | 20 May 2020, 17:03:20 UTC | Update README.md | 20 May 2020, 17:03:20 UTC |
| 715c79a | Lilian Janin | 20 May 2020, 16:57:21 UTC | Update README.md | 20 May 2020, 16:57:21 UTC |
| eab46ef | Lilian Janin | 14 June 2019, 10:57:56 UTC | Trying to make it compile with ubuntu:18.04 | 14 June 2019, 10:57:56 UTC |
| 1f995e5 | Lilian Janin | 10 September 2018, 09:12:10 UTC | Update README.md | 10 September 2018, 09:12:10 UTC |
| 8cb41fd | Lilian Janin | 04 September 2018, 15:47:02 UTC | Update README.md | 04 September 2018, 15:47:02 UTC |
| 1452b38 | Lilian Janin | 04 September 2018, 15:45:34 UTC | Links to HTML doc | 04 September 2018, 15:45:34 UTC |
| edb2c08 | Lilian Janin | 04 September 2018, 15:24:14 UTC | Issue #6: global2local throws error due to PNEXT<0 | 04 September 2018, 15:24:14 UTC |
| 1680ed2 | Lilian Janin | 17 August 2018, 14:12:25 UTC | Changing read names in BAM output, so that Firebrand doesn't crash | 17 August 2018, 14:12:25 UTC |
| 0e15990 | Lilian Janin | 16 August 2018, 21:10:40 UTC | GC bias: Only consider the first and last 150 bases, to make the GC% values less average and to match a bit more closely Firebrand's GC plots, which are calculated using 150bp windows | 16 August 2018, 21:10:40 UTC |
| 7422263 | Lilian Janin | 16 August 2018, 13:06:23 UTC | New quality table generator, in BamAnalyser, and as new FastqAnalyser tool | 16 August 2018, 13:06:23 UTC |
| eb37cad | Lilian Janin | 10 August 2018, 21:24:47 UTC | We skip SV variants that don't pass, because they make too many good SNPs disappear | 10 August 2018, 21:24:47 UTC |
| e8356bb | Lilian Janin | 10 August 2018, 20:58:04 UTC | Removing homref variants | 10 August 2018, 20:58:04 UTC |
| 5a90e36 | Lilian Janin | 10 August 2018, 14:58:28 UTC | New tool to convert SV VCF to translocation-style VCF | 10 August 2018, 14:58:28 UTC |
| bd8846f | Lilian Janin | 08 August 2018, 21:08:47 UTC | Merge pull request #8 from sequencing/branch_fastq_output Branch fastq output | 08 August 2018, 21:08:47 UTC |
| 9e996eb | Lilian Janin | 08 August 2018, 17:29:39 UTC | Fixing same bug as before, but in the soft-clipping area | 08 August 2018, 17:29:39 UTC |
| 1bc6c6a | Lilian Janin | 07 August 2018, 21:00:24 UTC | Fixed bug where CIGAR string would become corrupted when indel variants would fall in the middle of indel errors | 07 August 2018, 21:00:24 UTC |
| a65dc8e | Lilian Janin | 07 August 2018, 17:24:38 UTC | Fixing bug where 2 consecutive 1-base deletions would sometimes get swapped and crash | 07 August 2018, 17:24:38 UTC |
| 57b7bf8 | Lilian Janin | 03 August 2018, 13:51:45 UTC | Re-increasing Xcoord length, as it wasn't the cause of a bug | 03 August 2018, 13:51:45 UTC |
| e3d325d | Lilian Janin | 03 August 2018, 11:06:15 UTC | FASTQ output: don't output reads that don't pass filter | 03 August 2018, 11:06:15 UTC |
| be76183 | Lilian Janin | 03 August 2018, 10:59:23 UTC | Smaller X coordinates in read names | 03 August 2018, 10:59:23 UTC |
| d0a5aaf | Lilian Janin | 03 August 2018, 09:31:43 UTC | New 2x150 RunInfo file | 03 August 2018, 09:31:43 UTC |
| 38f2372 | Lilian Janin | 01 August 2018, 17:16:52 UTC | Unifying Run Id in all RunInfo files | 01 August 2018, 17:16:52 UTC |
| 930d890 | Lilian Janin | 01 August 2018, 13:10:25 UTC | Don't trim the last base from FASTQ reads. Reduced verbosity. | 01 August 2018, 13:10:25 UTC |
| 5f50232 | Lilian Janin | 31 July 2018, 20:33:42 UTC | Making FASTQ read names unique | 31 July 2018, 20:33:42 UTC |
| 1138309 | Lilian Janin | 31 July 2018, 13:09:45 UTC | Include position in FASTQ read names | 31 July 2018, 13:09:45 UTC |
| 1a4238d | Lilian Janin | 31 July 2018, 10:58:46 UTC | FASTQ output | 31 July 2018, 10:58:46 UTC |
| 32177d3 | Lilian Janin | 30 July 2018, 22:00:15 UTC | Initial commit: support for FASTQ output | 30 July 2018, 22:00:15 UTC |
| 1c970b1 | Lilian Janin | 30 July 2018, 17:13:05 UTC | Version bump | 30 July 2018, 17:13:05 UTC |
| 8080f77 | Lilian Janin | 30 July 2018, 17:12:37 UTC | quality score was becoming negative | 30 July 2018, 17:12:37 UTC |
| 39a4300 | Lilian Janin | 22 February 2018, 12:10:47 UTC | Missing header | 22 February 2018, 12:10:47 UTC |
| b62bcc7 | Lilian Janin | 08 February 2018, 15:10:52 UTC | Update README.md | 08 February 2018, 15:10:52 UTC |
| 7d9cbd0 | Lilian Janin | 08 February 2018, 14:20:48 UTC | Fixed issue #2: boost 1.56.0 not supported Boost 1.56+ now required Removed warnings | 08 February 2018, 14:20:48 UTC |
| c6c78a8 | Lilian Janin | 08 February 2018, 13:40:34 UTC | Fix to allow cmake v3+ | 08 February 2018, 13:40:34 UTC |
| 5639ea1 | Lilian Janin | 08 February 2018, 13:07:47 UTC | Update README.md | 08 February 2018, 13:07:47 UTC |
| e26d014 | Lilian Janin | 08 February 2018, 11:42:52 UTC | Update README.md | 08 February 2018, 11:42:52 UTC |
| 5a3b570 | Lilian Janin | 08 February 2018, 11:42:27 UTC | Update README.md | 08 February 2018, 11:42:27 UTC |
| a321513 | Lilian Janin | 23 August 2017, 09:09:51 UTC | Fix when contigs are smaller than max template length (defined in --template-length-table) | 23 August 2017, 09:16:59 UTC |
| 946c065 | Lilian Janin | 23 December 2016, 13:50:05 UTC | Fixing fragment merge for tumour+normal workflow | 23 December 2016, 13:50:05 UTC |
| edb770b | Lilian Janin | 23 December 2016, 10:19:31 UTC | Removing hard-coded path | 23 December 2016, 10:19:31 UTC |
| a4cfd6d | Lilian Janin | 04 July 2016, 15:29:46 UTC | Updated configureEAGLE_Normal+Tumour.pl: typos, and set default tumour-purity to 1 instead of 0 | 04 July 2016, 15:29:46 UTC |
| 9ccebf9 | Lilian Janin | 08 June 2016, 09:31:45 UTC | Allow qscores<2 in quality table files. Any generated qscore <2 gets set to 2, rather than triggering an assert | 08 June 2016, 09:31:45 UTC |
| 3ee6590 | Lilian Janin | 16 March 2016, 09:17:42 UTC | Fixed crash when GT==./. | 16 March 2016, 09:17:42 UTC |
| 0aacdec | Lilian Janin | 07 January 2016, 09:15:41 UTC | GITHUB-3: Fixed invalid CIGAR string when a sequencing error was happening on top of a VCF insertion | 07 January 2016, 09:15:41 UTC |
| 1d90000 | Lilian Janin | 02 October 2015, 10:06:40 UTC | Fixed incorrect /bin/env shebangs | 02 October 2015, 10:06:40 UTC |
| 029a55f | Lilian Janin | 28 September 2015, 10:44:17 UTC | Adding bzip2 dependency, as it is not installed by default in some linux distribs | 28 September 2015, 10:44:17 UTC |
| f920290 | Lilian Janin | 28 September 2015, 10:41:21 UTC | Boost parser was sometimes failing when LOCALE wasn't defined. Now forcing it to be defined. | 28 September 2015, 10:41:21 UTC |
| 018cfd3 | Lilian Janin | 27 September 2015, 17:07:09 UTC | Updating dependencies install instructions | 27 September 2015, 17:07:09 UTC |
| 8b2669d | Lilian Janin | 27 September 2015, 16:36:44 UTC | Removing the need for bzip2 lib | 27 September 2015, 16:36:44 UTC |
| 63c31c5 | Lilian Janin | 26 September 2015, 23:03:50 UTC | Increasing patch version number | 26 September 2015, 23:03:50 UTC |
| ad4f8d0 | Lilian Janin | 26 September 2015, 23:00:52 UTC | Bugfix, when the last entry of the fragment index was in use, it was refering to the wrong fragment entry, usually followed by a crash | 26 September 2015, 23:00:52 UTC |
| 65d2e88 | Lilian Janin | 26 September 2015, 22:57:06 UTC | Several fixes that I found in an old directory | 26 September 2015, 22:57:06 UTC |
| 73d189c | Lilian Janin | 17 September 2014, 12:06:57 UTC | "make bam" now works with weird chromosome names containing pipe characters | 17 September 2014, 12:06:57 UTC |
| 772d70c | Lilian Janin | 17 September 2014, 11:40:50 UTC | Added metagenomics simulation use case | 17 September 2014, 11:40:50 UTC |
| e1e06fe | Lilian Janin | 29 August 2014, 14:54:15 UTC | Format fix | 29 August 2014, 14:54:15 UTC |
| 96deae7 | Lilian Janin | 29 August 2014, 14:52:54 UTC | Updated description | 29 August 2014, 14:52:54 UTC |
| 4e8a496 | Lilian Janin | 29 August 2014, 14:35:54 UTC | EAGLE 2.0: Public release under BSD License | 29 August 2014, 14:35:54 UTC |
| 1a18b11 | Lilian Janin | 28 August 2014, 12:19:03 UTC | Initial commit | 28 August 2014, 12:19:03 UTC |
