| e7bae5c | Polina Drozdova | 25 January 2018, 15:26:45 UTC | added pRS alignments | 25 January 2018, 15:26:45 UTC |
| 1ce6794 | Polina Drozdova | 25 January 2018, 11:54:01 UTC | updated README (tsv export) | 25 January 2018, 11:54:01 UTC |
| 1cb42a3 | Polina Drozdova | 25 January 2018, 11:50:47 UTC | readme.md | 25 January 2018, 11:50:47 UTC |
| 4fae3d0 | Polina Drozdova | 25 January 2018, 11:49:16 UTC | now also exports a tab-separated table in UGENE format | 25 January 2018, 11:49:16 UTC |
| 2d46d4f | Polina Drozdova | 25 January 2018, 10:14:00 UTC | more comments! | 25 January 2018, 10:14:00 UTC |
| 8fbb08a | Polina Drozdova | 24 January 2018, 16:12:26 UTC | now annotator finds features starting at position 1(0) | 24 January 2018, 16:12:26 UTC |
| 48614be | Polina Drozdova | 23 January 2018, 13:28:27 UTC | fixed a small bug (corrected files are now saved in the corrected_maps/ folder) | 23 January 2018, 13:28:27 UTC |
| f2b10f4 | Polina Drozdova | 23 January 2018, 13:21:13 UTC | expanded README + added sample data | 23 January 2018, 13:21:13 UTC |
| 08d8822 | Polina Drozdova | 23 January 2018, 13:00:34 UTC | added new diff dictionary | 23 January 2018, 13:00:34 UTC |
| 5b0886f | Polina Drozdova | 23 January 2018, 08:17:48 UTC | fixed a small bug (now exits if no file provided) | 23 January 2018, 08:17:48 UTC |
| 47bc7e9 | Polina Drozdova | 18 January 2018, 08:10:32 UTC | added the possibility to use user-provided name for the new plasmid | 18 January 2018, 08:10:32 UTC |
| 3301c80 | Polina Drozdova | 18 January 2018, 08:09:51 UTC | garbage removal | 18 January 2018, 08:09:51 UTC |
| 473a04c | Polina Drozdova | 18 January 2018, 07:53:05 UTC | placed all files into one folder | 18 January 2018, 07:53:05 UTC |
| 798c2ea | Polina Drozdova | 18 January 2018, 07:39:36 UTC | created README | 18 January 2018, 07:39:36 UTC |
| 69c7fbb | Polina Drozdova | 17 January 2018, 06:52:02 UTC | added conversion table / dictionary for pRS plasmids | 17 January 2018, 06:52:02 UTC |
| 89c8168 | Polina Drozdova | 15 January 2018, 14:59:03 UTC | Now better work with filepaths and messages | 15 January 2018, 14:59:03 UTC |
| 470f819 | Polina Drozdova | 15 January 2018, 14:15:33 UTC | now pRS corrector removes all annotations (add them with annotator) | 15 January 2018, 14:15:33 UTC |
| f3eb817 | Polina Drozdova | 15 January 2018, 14:13:25 UTC | +the previous one | 15 January 2018, 14:13:25 UTC |
| 699ef5c | Polina Drozdova | 15 January 2018, 14:09:13 UTC | restructured genbank-related scripts | 15 January 2018, 14:09:13 UTC |
| d2004e3 | Polina Drozdova | 03 January 2018, 08:16:12 UTC | added some genbank manipulation | 03 January 2018, 08:16:12 UTC |
| 68a086f | Polina Drozdova | 04 March 2016, 10:44:21 UTC | added description of correct_coord.py | 04 March 2016, 10:44:21 UTC |
| 7746c00 | Polina Drozdova | 04 March 2016, 06:22:59 UTC | some cleanup, better argument handling, and special solution for 0-based bed coordinates | 04 March 2016, 06:22:59 UTC |
| 0429b6b | Polina Drozdova | 03 March 2016, 12:13:35 UTC | corrected representation of ints as strings | 03 March 2016, 12:13:35 UTC |
| a6d4966 | Polina Drozdova | 03 March 2016, 11:52:35 UTC | minor changes | 03 March 2016, 11:52:35 UTC |
| 6e7bd89 | Polina Drozdova | 03 March 2016, 11:52:03 UTC | now coordinate correction works with bed | 03 March 2016, 11:52:03 UTC |
| 9e7c1ea | Polina Drozdova | 03 March 2016, 11:43:01 UTC | added a quick and dirty decision for flipped coordinates in gff | 03 March 2016, 11:43:01 UTC |
| 9e41519 | Polina Drozdova | 08 October 2015, 20:49:07 UTC | updated README | 08 October 2015, 20:49:07 UTC |
| 35fee92 | Polina Drozdova | 01 October 2015, 19:33:07 UTC | fixed an ugly bug that multiplied annotations for the first gene on each contig | 01 October 2015, 19:33:07 UTC |
| e5fbe5d | Polina Drozdova | 22 August 2015, 20:35:58 UTC | updated README to comment on new scripts and additional functions in older scripts | 22 August 2015, 20:35:58 UTC |
| 873d485 | Polina Drozdova | 22 August 2015, 20:34:32 UTC | fixed some issues in rename_gff_by_table.py | 22 August 2015, 20:34:32 UTC |
| d0168e8 | Polina Drozdova | 14 August 2015, 15:50:32 UTC | fixed a small bug which multiplied working time of gff_to_bed by # lines | 14 August 2015, 15:50:32 UTC |
| aa4c120 | Polina Drozdova | 14 August 2015, 11:21:17 UTC | updated renamer by table (now more flexible) | 14 August 2015, 11:21:17 UTC |
| 9cd9703 | Polina Drozdova | 03 August 2015, 14:43:28 UTC | added gff renamer with proteinortho output | 03 August 2015, 14:43:28 UTC |
| a37f198 | Polina Drozdova | 26 July 2015, 17:02:43 UTC | added quick simple tests (I'll just leave it here) | 26 July 2015, 17:02:43 UTC |
| a871666 | Polina Drozdova | 26 July 2015, 17:00:57 UTC | tests.py now with unittest | 26 July 2015, 17:00:57 UTC |
| 95e20d0 | Polina Drozdova | 14 July 2015, 08:39:23 UTC | now writing long bed is a possible (and default) option in conversion.py (maintenance commit) | 14 July 2015, 08:39:23 UTC |
| f8ed4b2 | Polina Drozdova | 14 July 2015, 08:33:50 UTC | added code to deal with vcf4.2 to vcf4.1 conversion (maintenance commit) | 14 July 2015, 08:33:50 UTC |
| a4fc650 | Polina Drozdova | 05 July 2015, 20:40:37 UTC | added gff renaming script (maintenance commit) | 05 July 2015, 20:40:37 UTC |
| dde742a | Polina Drozdova | 29 June 2015, 13:59:31 UTC | finally fixed the cds-only issue (review commit) | 29 June 2015, 13:59:31 UTC |
| 84e6416 | Polina Drozdova | 29 June 2015, 08:15:37 UTC | fixed cds-only mode in gtf_to_gff3 (review commit) | 29 June 2015, 08:15:37 UTC |
| ab47535 | Polina Drozdova | 28 June 2015, 21:26:16 UTC | updated conversion.py; now reading input files is outside of functions (review commit) | 28 June 2015, 21:26:16 UTC |
| c182e25 | Polina Drozdova | 26 June 2015, 18:25:13 UTC | updated argument parsing and fixed minor problems in conversion.py (review commit) | 26 June 2015, 18:25:13 UTC |
| 16b20b1 | Polina Drozdova | 26 June 2015, 10:27:23 UTC | conversion.py now with argparse (review commit) | 26 June 2015, 10:27:23 UTC |
| b09a14b | Polina Drozdova | 26 June 2015, 10:01:59 UTC | modified .gitignore (maintenance commit) | 26 June 2015, 10:01:59 UTC |
| ebeb9f4 | Polina Drozdova | 26 June 2015, 10:01:01 UTC | removed unnecessary files (maintenance commit | 26 June 2015, 10:01:01 UTC |
| c0882d9 | Polina Drozdova | 19 June 2015, 15:20:17 UTC | updated write_tsv in io_tools (review commit) | 19 June 2015, 15:20:17 UTC |
| 68a7b4d | Polina Drozdova | 19 June 2015, 08:59:06 UTC | updated compare_vcf.py according to the notes (review commit) | 19 June 2015, 09:00:27 UTC |
| 8fa85b8 | Polina Drozdova | 08 June 2015, 11:29:57 UTC | compare_vcf now with a function for comparison (review commit) | 08 June 2015, 11:29:57 UTC |
| 7a1174e | Polina Drozdova | 08 June 2015, 11:14:52 UTC | added a possibility to write to stdout | 08 June 2015, 11:14:52 UTC |
| 2fc9232 | Polina Drozdova | 08 June 2015, 11:12:12 UTC | updated examples (maintenance commit) | 08 June 2015, 11:12:12 UTC |
| 274e062 | Polina Drozdova | 27 May 2015, 07:42:50 UTC | here it works (restore point) (maintenance commit | 27 May 2015, 07:42:50 UTC |
| fdf66d3 | Polina Drozdova | 27 May 2015, 07:40:46 UTC | updated test files (made shorter) (maintenance commit) | 27 May 2015, 07:40:46 UTC |
| 6a5798e | Polina Drozdova | 19 May 2015, 11:03:16 UTC | added simple tests (review commit) | 19 May 2015, 11:03:16 UTC |
| c8a3397 | Polina Drozdova | 19 May 2015, 11:01:08 UTC | changed names of base functions (maintenance commit) | 19 May 2015, 11:01:08 UTC |
| 524ef51 | Polina Drozdova | 18 May 2015, 17:27:15 UTC | updated temporary files (maintenance commit) | 18 May 2015, 17:27:15 UTC |
| aae98fe | Polina Drozdova | 18 May 2015, 17:24:43 UTC | minor changes to conversion.py (maintenance commit) | 18 May 2015, 17:24:43 UTC |
| c00e3e2 | Polina Drozdova | 18 May 2015, 17:23:48 UTC | made handy functions an importable module | 18 May 2015, 17:23:48 UTC |
| b26165d | Polina Drozdova | 09 May 2015, 12:31:54 UTC | added command line argument parsing (review commit) | 09 May 2015, 12:31:54 UTC |
| 34a66a7 | Polina Drozdova | 09 May 2015, 11:12:24 UTC | fixed some minor bugs in conversion.py (maintenance commit) | 09 May 2015, 11:12:24 UTC |
| 44780fb | Polina Drozdova | 07 May 2015, 17:17:45 UTC | fixed line breaks + some other problems (review commit) | 07 May 2015, 17:17:45 UTC |
| 0023cc6 | Polina Drozdova | 07 May 2015, 16:37:35 UTC | added examples of gtf, gff2, gff3, and bed (maintenance commit) | 07 May 2015, 16:37:35 UTC |
| 6b39f11 | Polina Drozdova | 07 May 2015, 16:35:31 UTC | minor changes to README (formatting) (maintenance commit) | 07 May 2015, 16:35:31 UTC |
| 3dbfdb1 | Polina Drozdova | 04 May 2015, 10:21:22 UTC | first draft of conversion.py (read_tsv, write_tsv, gtf2gff3, gff2bed) (review commit) | 04 May 2015, 10:21:22 UTC |
| bc4e056 | Polina Drozdova | 03 May 2015, 20:02:30 UTC | conversion.py, the first draft (maintenance commit | 03 May 2015, 20:02:30 UTC |
| 1b5e54d | Polina Drozdova | 03 May 2015, 11:32:05 UTC | added some information about file formats to README (maintenance commit) | 03 May 2015, 11:32:05 UTC |
| 165789f | Polina Drozdova | 26 April 2015, 10:05:15 UTC | minor revision of compare_vcf.py (maintenance commit) | 26 April 2015, 10:05:15 UTC |
| 9b46a84 | Polina Drozdova | 26 April 2015, 10:03:48 UTC | removed duplicated files (maintenance commit) | 26 April 2015, 10:03:48 UTC |
| f841e41 | Polina Drozdova | 26 April 2015, 09:37:19 UTC | speedup for compare_vcf.py (review commit) | 26 April 2015, 09:37:19 UTC |
| d85397a | Polina Drozdova | 25 April 2015, 20:08:05 UTC | revised lexicoSV.py (review commit) | 25 April 2015, 20:08:05 UTC |
| cba8a41 | Polina Drozdova | 25 April 2015, 19:53:06 UTC | revised compare_vcf.py (review commit) | 25 April 2015, 19:53:06 UTC |
| 722d498 | Polina Drozdova | 24 April 2015, 21:36:37 UTC | minor updates to README (maintenance commit) | 24 April 2015, 21:36:37 UTC |
| 16bef0f | Polina Drozdova | 24 April 2015, 20:46:49 UTC | added some background info and useful links (maintenance commit) | 24 April 2015, 20:46:49 UTC |
| 6e5afcf | Polina Drozdova | 24 April 2015, 20:45:42 UTC | revised compare_vcf.py and lexicoSV.py (review commit) | 24 April 2015, 20:45:42 UTC |
| 9090a82 | Polina Drozdova | 24 April 2015, 20:44:39 UTC | updated README (review commit) | 24 April 2015, 20:44:39 UTC |
| 71086b4 | Polina Drozdova | 19 April 2015, 10:22:15 UTC | updated examples (maintenance commit) | 19 April 2015, 10:22:15 UTC |
| 8f10342 | Polina Drozdova | 19 April 2015, 10:21:30 UTC | beta versions of compare_vcf and lexicoSV (review commit) | 19 April 2015, 10:21:30 UTC |
| 45f923f | Polina Drozdova | 19 April 2015, 07:16:47 UTC | updated README (maintenance commit) | 19 April 2015, 07:16:47 UTC |
| f679901 | Polina Drozdova | 19 April 2015, 07:14:34 UTC | updated README (maintenance commit) | 19 April 2015, 07:14:34 UTC |
| 1307a06 | Polina Drozdova | 19 April 2015, 07:12:28 UTC | updated README (maintenance commit) | 19 April 2015, 07:12:28 UTC |
| ed73c40 | Polina Drozdova | 17 April 2015, 20:17:39 UTC | updated compare_vcf.py and added example data | 17 April 2015, 20:17:39 UTC |
| d8e1f53 | Polina Drozdova | 17 April 2015, 20:08:55 UTC | added the scripts as is | 17 April 2015, 20:08:55 UTC |
| f7b96af | Polina Drozdova | 12 April 2015, 06:14:02 UTC | added gitignore | 12 April 2015, 06:14:02 UTC |
| 804a238 | Polina Drozdova | 12 April 2015, 06:00:18 UTC | initial commit + readme | 12 April 2015, 06:00:18 UTC |
