| 8d58eaf | Mikhail Kolmogorov | 04 November 2015, 22:33:06 UTC | minor refactoring | 04 November 2015, 22:33:06 UTC |
| 246ddba | Mikhail Kolmogorov | 04 November 2015, 03:56:48 UTC | a fix for gap estimation | 04 November 2015, 03:56:48 UTC |
| 596d7c0 | Mikhail Kolmogorov | 01 November 2015, 02:40:24 UTC | some refactoring | 01 November 2015, 02:40:24 UTC |
| 1a3ae32 | Son Pham | 30 October 2015, 21:37:12 UTC | Update README.md | 30 October 2015, 21:37:12 UTC |
| f37511c | Mikhail Kolmogorov | 29 September 2015, 00:25:49 UTC | minor docs change | 29 September 2015, 00:25:49 UTC |
| 19d3ad4 | Mikhail Kolmogorov | 29 September 2015, 00:08:17 UTC | wrong date | 29 September 2015, 00:08:17 UTC |
| 2284233 | Mikhail Kolmogorov | 29 September 2015, 00:07:33 UTC | 1.2 | 29 September 2015, 00:07:33 UTC |
| bdcccea | Mikhail Kolmogorov | 28 September 2015, 23:46:25 UTC | Merge branch 'devel' | 28 September 2015, 23:46:25 UTC |
| fd9b35c | Mikhail Kolmogorov | 28 September 2015, 23:46:14 UTC | minor | 28 September 2015, 23:46:14 UTC |
| fa6f861 | Mikhail Kolmogorov | 28 September 2015, 23:31:21 UTC | Merge branch 'devel' of https://github.com/fenderglass/Ragout into devel | 28 September 2015, 23:31:21 UTC |
| 0a93120 | Mikhail Kolmogorov | 28 September 2015, 23:31:02 UTC | a fix for empty links information | 28 September 2015, 23:31:02 UTC |
| eb1692c | Mikhail Kolmogorov | 28 September 2015, 18:38:57 UTC | documantation improved | 28 September 2015, 18:38:57 UTC |
| 04bb6e1 | Mikhail Kolmogorov | 25 September 2015, 20:57:32 UTC | priority queue removed | 25 September 2015, 20:57:32 UTC |
| 2861ecb | Mikhail Kolmogorov | 25 September 2015, 20:44:56 UTC | a fix in rearrangement projection | 25 September 2015, 20:44:56 UTC |
| a3bd4e5 | Mikhail Kolmogorov | 25 September 2015, 01:00:30 UTC | output generator refactoring | 25 September 2015, 01:00:30 UTC |
| 1338e4b | Mikhail Kolmogorov | 24 September 2015, 02:04:50 UTC | partially unplaced contigs | 24 September 2015, 02:04:50 UTC |
| 581be6b | Mikhail Kolmogorov | 24 September 2015, 01:43:37 UTC | deterministic tree construction + fix in sorting by tree distance | 24 September 2015, 01:43:37 UTC |
| 545c417 | Mikhail Kolmogorov | 24 September 2015, 01:42:03 UTC | script renaming | 24 September 2015, 01:42:03 UTC |
| 061828f | Mikhail Kolmogorov | 12 September 2015, 14:18:04 UTC | chromosome names in support fields | 12 September 2015, 14:18:04 UTC |
| 03e5624 | Mikhail Kolmogorov | 12 September 2015, 12:15:21 UTC | ragout version in log | 12 September 2015, 12:15:21 UTC |
| be33c34 | Mikhail Kolmogorov | 09 September 2015, 16:55:11 UTC | small fix for merge algorithm | 09 September 2015, 16:55:11 UTC |
| 3c142fd | Mikhail Kolmogorov | 09 September 2015, 16:40:21 UTC | a fix for one-contig scaffolds | 09 September 2015, 16:40:21 UTC |
| 610f222 | Mikhail Kolmogorov | 25 August 2015, 17:46:15 UTC | beta version notice | 25 August 2015, 17:46:15 UTC |
| 11c2a94 | Mikhail Kolmogorov | 25 August 2015, 17:29:16 UTC | Merge branch 'devel' into path_cover Syncronizing branches | 25 August 2015, 17:29:16 UTC |
| 9780da0 | Mikhail Kolmogorov | 25 August 2015, 17:17:56 UTC | minor documentation change | 25 August 2015, 17:17:56 UTC |
| 3b9522a | Mikhail Kolmogorov | 20 August 2015, 11:49:14 UTC | fixed one-contig scaffolds | 20 August 2015, 11:49:14 UTC |
| 8a30ee7 | Mikhail Kolmogorov | 19 August 2015, 10:33:47 UTC | handling scaffolds from a single fragment | 19 August 2015, 10:33:47 UTC |
| 500b10e | Mikhail Kolmogorov | 18 August 2015, 10:55:51 UTC | documentation improved | 18 August 2015, 10:55:51 UTC |
| f85b758 | Mikhail Kolmogorov | 10 August 2015, 16:42:11 UTC | naming reference as closest in the tree, distance estimation with tree | 10 August 2015, 16:42:11 UTC |
| 4f77e88 | Mikhail Kolmogorov | 10 August 2015, 09:50:38 UTC | typo | 10 August 2015, 09:50:38 UTC |
| 6382865 | Mikhail Kolmogorov | 10 August 2015, 09:45:17 UTC | some refactoring | 10 August 2015, 09:45:17 UTC |
| 3e1ab6d | Mikhail Kolmogorov | 05 August 2015, 10:39:57 UTC | improved statistics output | 05 August 2015, 10:39:57 UTC |
| 289b958 | Mikhail Kolmogorov | 05 August 2015, 09:49:25 UTC | maximum gap size, improved chomsomsome naming | 05 August 2015, 09:49:25 UTC |
| 860c877 | Mikhail Kolmogorov | 04 August 2015, 10:39:05 UTC | small fix for rearrangement projection | 04 August 2015, 10:39:05 UTC |
| 1e4b01d | Mikhail Kolmogorov | 01 August 2015, 15:55:20 UTC | correct links handling while reversing scaffold strand | 01 August 2015, 15:55:20 UTC |
| 802bfcf | Mikhail Kolmogorov | 01 August 2015, 14:11:07 UTC | reference strand + AGP output | 01 August 2015, 14:11:07 UTC |
| 062b14c | Mikhail Kolmogorov | 31 July 2015, 10:55:55 UTC | no negative gaps | 31 July 2015, 10:55:55 UTC |
| fc2dc70 | Mikhail Kolmogorov | 30 July 2015, 11:19:41 UTC | keep chromosomal structure while projecting rearrangements | 30 July 2015, 11:19:41 UTC |
| 792b8b9 | Mikhail Kolmogorov | 20 July 2015, 21:27:16 UTC | new rearrangement policy | 20 July 2015, 21:27:16 UTC |
| 16acbb1 | Mikhail Kolmogorov | 10 July 2015, 02:11:36 UTC | Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover | 10 July 2015, 02:11:36 UTC |
| 6106ec3 | Mikhail Kolmogorov | 10 July 2015, 02:11:18 UTC | improved chromosome report script | 10 July 2015, 02:11:18 UTC |
| f6ba892 | Mikhail Kolmogorov | 10 July 2015, 02:08:54 UTC | Merge branch 'path_cover' of github.com:fenderglass/Ragout into path_cover | 10 July 2015, 02:08:54 UTC |
| 406e8aa | Mikhail Kolmogorov | 10 July 2015, 02:08:44 UTC | static linkage + smarter rearrangement projection | 10 July 2015, 02:08:44 UTC |
| 71e5d02 | Mikhail Kolmogorov | 19 June 2015, 23:08:02 UTC | Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover | 19 June 2015, 23:08:02 UTC |
| b50bffe | Mikhail Kolmogorov | 19 June 2015, 23:07:41 UTC | tweak in RR | 19 June 2015, 23:07:41 UTC |
| fb59a4f | Mikhail Kolmogorov | 19 June 2015, 23:07:33 UTC | minor stuff | 19 June 2015, 23:07:33 UTC |
| c56c510 | Mikhail Kolmogorov | 19 June 2015, 01:28:20 UTC | strand as in naming genome + chimeras through infinity edges | 19 June 2015, 01:28:20 UTC |
| e524a69 | Mikhail Kolmogorov | 18 June 2015, 19:46:32 UTC | turning of renumeration of unique repeats | 18 June 2015, 19:46:32 UTC |
| 1f57e6f | Mikhail Kolmogorov | 17 June 2015, 01:04:26 UTC | lowcase characters in fasta | 17 June 2015, 01:04:26 UTC |
| ed423ee | Mikhail Kolmogorov | 16 June 2015, 00:39:30 UTC | Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover | 16 June 2015, 00:39:30 UTC |
| 741a080 | Mikhail Kolmogorov | 16 June 2015, 00:38:59 UTC | repeats resolving slightly improved | 16 June 2015, 00:38:59 UTC |
| 0e52269 | Mikhail Kolmogorov | 13 June 2015, 21:09:43 UTC | tests working again | 13 June 2015, 21:09:43 UTC |
| 61b6952 | Mikhail Kolmogorov | 12 June 2015, 01:36:12 UTC | cycle distance test | 12 June 2015, 01:36:12 UTC |
| b4739b7 | Mikhail Kolmogorov | 09 June 2015, 22:39:10 UTC | fix in gap calculating | 09 June 2015, 22:39:10 UTC |
| 49a46b1 | Mikhail Kolmogorov | 09 June 2015, 19:01:48 UTC | naming_ref parameter + unlocalized contigs output | 09 June 2015, 19:01:48 UTC |
| d5afacc | Mikhail Kolmogorov | 08 June 2015, 18:58:53 UTC | fix? | 08 June 2015, 18:58:53 UTC |
| c1d1ca8 | Mikhail Kolmogorov | 07 June 2015, 21:54:18 UTC | chromosome naming (ad-hoc version) | 07 June 2015, 21:54:18 UTC |
| 5626517 | Mikhail Kolmogorov | 30 May 2015, 03:08:21 UTC | run stages abstraction | 30 May 2015, 03:08:21 UTC |
| 8231d56 | Mikhail Kolmogorov | 30 May 2015, 02:21:56 UTC | logging + chromosome script | 30 May 2015, 02:21:56 UTC |
| 79b20f7 | Mikhail Kolmogorov | 26 May 2015, 19:05:33 UTC | chromosome fusions script | 26 May 2015, 19:05:33 UTC |
| b214415 | Mikhail Kolmogorov | 26 May 2015, 02:06:52 UTC | debugging improvements | 26 May 2015, 02:06:52 UTC |
| 42a3c5d | Mikhail Kolmogorov | 25 May 2015, 20:34:47 UTC | k-breaks and some fixes in output generation and contig breaks | 25 May 2015, 20:34:47 UTC |
| 893a76f | Mikhail Kolmogorov | 23 May 2015, 20:35:59 UTC | fix in rearrangements projecting | 23 May 2015, 20:35:59 UTC |
| 61e3e3e | Mikhail Kolmogorov | 22 May 2015, 20:17:24 UTC | inferer instead of refiner on the last stage | 22 May 2015, 20:17:24 UTC |
| a3a0dd2 | Mikhail Kolmogorov | 22 May 2015, 04:18:32 UTC | more accurate adjacency refinement | 22 May 2015, 04:18:32 UTC |
| e0d3f3e | Mikhail Kolmogorov | 22 May 2015, 02:52:41 UTC | more accurate low-level scaffold structure | 22 May 2015, 02:52:41 UTC |
| 0627959 | Mikhail Kolmogorov | 21 May 2015, 00:35:25 UTC | debug dir fix | 21 May 2015, 00:35:25 UTC |
| 91bacb8 | Mikhail Kolmogorov | 21 May 2015, 00:30:52 UTC | correct contig links for refiner module | 21 May 2015, 00:30:52 UTC |
| 536a1fd | Mikhail Kolmogorov | 18 May 2015, 00:45:14 UTC | conservative assembly + refinement in the end + partial fix of distance estimation | 18 May 2015, 00:45:14 UTC |
| ed8ec16 | Mikhail Kolmogorov | 17 May 2015, 02:20:12 UTC | small fix in rearrangement projection + Helicobacter test removed | 17 May 2015, 02:20:12 UTC |
| 8011ca8 | Mikhail Kolmogorov | 17 May 2015, 01:55:57 UTC | some adjustments + fixed distances and supporting genomes | 17 May 2015, 01:55:57 UTC |
| 57143f6 | Mikhail Kolmogorov | 16 May 2015, 00:13:58 UTC | back to iterative BG + working rearrangements projection | 16 May 2015, 00:13:58 UTC |
| 681fbff | Mikhail Kolmogorov | 14 May 2015, 00:39:39 UTC | and adhoc implementation of rearrangement projection | 14 May 2015, 00:39:39 UTC |
| c8c62eb | Mikhail Kolmogorov | 13 May 2015, 02:41:16 UTC | iterative contig breaks | 13 May 2015, 02:41:16 UTC |
| b8a8432 | Mikhail Kolmogorov | 12 May 2015, 19:57:14 UTC | handling rare case in chimera detector | 12 May 2015, 19:57:14 UTC |
| 633c4c9 | Mikhail Kolmogorov | 12 May 2015, 01:35:59 UTC | iterative contig breakage | 12 May 2015, 01:35:59 UTC |
| 79c73f5 | Mikhail Kolmogorov | 09 May 2015, 06:11:41 UTC | inversions recognition | 09 May 2015, 06:11:41 UTC |
| 2a212a1 | Mikhail Kolmogorov | 08 May 2015, 20:29:04 UTC | some extra debug features | 08 May 2015, 20:29:04 UTC |
| dc9d0a7 | Mikhail Kolmogorov | 08 May 2015, 03:16:51 UTC | more relaxed chimera detection | 08 May 2015, 03:16:51 UTC |
| 43bd350 | Mikhail Kolmogorov | 07 May 2015, 02:35:44 UTC | minimum gap size | 07 May 2015, 02:35:44 UTC |
| 8a6cc58 | Mikhail Kolmogorov | 06 May 2015, 18:38:02 UTC | fix in alternating cycle search | 06 May 2015, 18:38:02 UTC |
| 5f61ed5 | Mikhail Kolmogorov | 06 May 2015, 04:50:59 UTC | slowness fixed | 06 May 2015, 04:50:59 UTC |
| e56a232 | Mikhail Kolmogorov | 06 May 2015, 00:08:32 UTC | faster chimer detection | 06 May 2015, 00:08:32 UTC |
| 48e26ab | Mikhail Kolmogorov | 05 May 2015, 23:21:22 UTC | some refactoring | 05 May 2015, 23:21:22 UTC |
| 8f07fce | Mikhail Kolmogorov | 05 May 2015, 22:17:54 UTC | draft sequences with rr | 05 May 2015, 22:17:54 UTC |
| a8eaa08 | Mikhail Kolmogorov | 01 May 2015, 21:39:28 UTC | bux with coordinates | 01 May 2015, 21:39:28 UTC |
| fbff3df | Mikhail Kolmogorov | 01 May 2015, 21:27:09 UTC | fasta statistics fix | 01 May 2015, 21:27:09 UTC |
| e02fc42 | Mikhail Kolmogorov | 01 May 2015, 20:46:33 UTC | cutting contigs + tests fix | 01 May 2015, 20:46:33 UTC |
| ccc6c22 | Mikhail Kolmogorov | 01 May 2015, 01:05:35 UTC | fix for debug mode | 01 May 2015, 01:05:35 UTC |
| d048f03 | Mikhail Kolmogorov | 01 May 2015, 00:12:57 UTC | fixed bug with permutation attributes | 01 May 2015, 00:12:57 UTC |
| 6e04d5c | Mikhail Kolmogorov | 30 April 2015, 23:54:26 UTC | new method for chimera detection | 30 April 2015, 23:54:26 UTC |
| 91cee0c | Mikhail Kolmogorov | 30 April 2015, 03:25:44 UTC | final refactoring | 30 April 2015, 03:25:44 UTC |
| 20d1c11 | Mikhail Kolmogorov | 29 April 2015, 22:23:30 UTC | major refactoring | 29 April 2015, 22:23:30 UTC |
| b4d82ec | Mikhail Kolmogorov | 29 April 2015, 02:03:33 UTC | keep only those blocks that represented exactly once at first stage | 29 April 2015, 02:03:33 UTC |
| 97ec218 | Mikhail Kolmogorov | 29 April 2015, 00:11:01 UTC | faster version + rr only on last stage | 29 April 2015, 00:11:01 UTC |
| 0af3bd1 | Mikhail Kolmogorov | 27 April 2015, 22:55:45 UTC | trying to incorporate canddidate adjacencies | 27 April 2015, 22:55:45 UTC |
| d342b92 | Mikhail Kolmogorov | 27 April 2015, 02:21:54 UTC | a fix for permutations from one block | 27 April 2015, 02:21:54 UTC |
| f9e01c6 | Mikhail Kolmogorov | 27 April 2015, 00:28:28 UTC | a working fix | 27 April 2015, 00:28:28 UTC |
| 45ea02d | Mikhail Kolmogorov | 25 April 2015, 22:54:31 UTC | not going through internal contigs' blocks | 25 April 2015, 22:54:31 UTC |
| 783cbf1 | Mikhail Kolmogorov | 25 April 2015, 21:33:36 UTC | fix for preferred edges heuristic | 25 April 2015, 21:33:36 UTC |
