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Revision Author Date Message Commit Date
f85b758 naming reference as closest in the tree, distance estimation with tree 10 August 2015, 16:42:11 UTC
4f77e88 typo 10 August 2015, 09:50:38 UTC
6382865 some refactoring 10 August 2015, 09:45:17 UTC
3e1ab6d improved statistics output 05 August 2015, 10:39:57 UTC
289b958 maximum gap size, improved chomsomsome naming 05 August 2015, 09:49:25 UTC
860c877 small fix for rearrangement projection 04 August 2015, 10:39:05 UTC
1e4b01d correct links handling while reversing scaffold strand 01 August 2015, 15:55:20 UTC
802bfcf reference strand + AGP output 01 August 2015, 14:11:07 UTC
062b14c no negative gaps 31 July 2015, 10:55:55 UTC
fc2dc70 keep chromosomal structure while projecting rearrangements 30 July 2015, 11:19:41 UTC
792b8b9 new rearrangement policy 20 July 2015, 21:27:16 UTC
16acbb1 Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover 10 July 2015, 02:11:36 UTC
6106ec3 improved chromosome report script 10 July 2015, 02:11:18 UTC
f6ba892 Merge branch 'path_cover' of github.com:fenderglass/Ragout into path_cover 10 July 2015, 02:08:54 UTC
406e8aa static linkage + smarter rearrangement projection 10 July 2015, 02:08:44 UTC
71e5d02 Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover 19 June 2015, 23:08:02 UTC
b50bffe tweak in RR 19 June 2015, 23:07:41 UTC
fb59a4f minor stuff 19 June 2015, 23:07:33 UTC
c56c510 strand as in naming genome + chimeras through infinity edges 19 June 2015, 01:28:20 UTC
e524a69 turning of renumeration of unique repeats 18 June 2015, 19:46:32 UTC
1f57e6f lowcase characters in fasta 17 June 2015, 01:04:26 UTC
ed423ee Merge branch 'path_cover' of https://github.com/fenderglass/Ragout into path_cover 16 June 2015, 00:39:30 UTC
741a080 repeats resolving slightly improved 16 June 2015, 00:38:59 UTC
0e52269 tests working again 13 June 2015, 21:09:43 UTC
61b6952 cycle distance test 12 June 2015, 01:36:12 UTC
b4739b7 fix in gap calculating 09 June 2015, 22:39:10 UTC
49a46b1 naming_ref parameter + unlocalized contigs output 09 June 2015, 19:01:48 UTC
d5afacc fix? 08 June 2015, 18:58:53 UTC
c1d1ca8 chromosome naming (ad-hoc version) 07 June 2015, 21:54:18 UTC
5626517 run stages abstraction 30 May 2015, 03:08:21 UTC
8231d56 logging + chromosome script 30 May 2015, 02:21:56 UTC
79b20f7 chromosome fusions script 26 May 2015, 19:05:33 UTC
b214415 debugging improvements 26 May 2015, 02:06:52 UTC
42a3c5d k-breaks and some fixes in output generation and contig breaks 25 May 2015, 20:34:47 UTC
893a76f fix in rearrangements projecting 23 May 2015, 20:35:59 UTC
61e3e3e inferer instead of refiner on the last stage 22 May 2015, 20:17:24 UTC
a3a0dd2 more accurate adjacency refinement 22 May 2015, 04:18:32 UTC
e0d3f3e more accurate low-level scaffold structure 22 May 2015, 02:52:41 UTC
0627959 debug dir fix 21 May 2015, 00:35:25 UTC
91bacb8 correct contig links for refiner module 21 May 2015, 00:30:52 UTC
536a1fd conservative assembly + refinement in the end + partial fix of distance estimation 18 May 2015, 00:45:14 UTC
ed8ec16 small fix in rearrangement projection + Helicobacter test removed 17 May 2015, 02:20:12 UTC
8011ca8 some adjustments + fixed distances and supporting genomes 17 May 2015, 01:55:57 UTC
57143f6 back to iterative BG + working rearrangements projection 16 May 2015, 00:13:58 UTC
681fbff and adhoc implementation of rearrangement projection 14 May 2015, 00:39:39 UTC
c8c62eb iterative contig breaks 13 May 2015, 02:41:16 UTC
b8a8432 handling rare case in chimera detector 12 May 2015, 19:57:14 UTC
633c4c9 iterative contig breakage 12 May 2015, 01:35:59 UTC
79c73f5 inversions recognition 09 May 2015, 06:11:41 UTC
2a212a1 some extra debug features 08 May 2015, 20:29:04 UTC
dc9d0a7 more relaxed chimera detection 08 May 2015, 03:16:51 UTC
43bd350 minimum gap size 07 May 2015, 02:35:44 UTC
8a6cc58 fix in alternating cycle search 06 May 2015, 18:38:02 UTC
5f61ed5 slowness fixed 06 May 2015, 04:50:59 UTC
e56a232 faster chimer detection 06 May 2015, 00:08:32 UTC
48e26ab some refactoring 05 May 2015, 23:21:22 UTC
8f07fce draft sequences with rr 05 May 2015, 22:17:54 UTC
a8eaa08 bux with coordinates 01 May 2015, 21:39:28 UTC
fbff3df fasta statistics fix 01 May 2015, 21:27:09 UTC
e02fc42 cutting contigs + tests fix 01 May 2015, 20:46:33 UTC
ccc6c22 fix for debug mode 01 May 2015, 01:05:35 UTC
d048f03 fixed bug with permutation attributes 01 May 2015, 00:12:57 UTC
6e04d5c new method for chimera detection 30 April 2015, 23:54:26 UTC
91cee0c final refactoring 30 April 2015, 03:25:44 UTC
20d1c11 major refactoring 29 April 2015, 22:23:30 UTC
b4d82ec keep only those blocks that represented exactly once at first stage 29 April 2015, 02:03:33 UTC
97ec218 faster version + rr only on last stage 29 April 2015, 00:11:01 UTC
0af3bd1 trying to incorporate canddidate adjacencies 27 April 2015, 22:55:45 UTC
d342b92 a fix for permutations from one block 27 April 2015, 02:21:54 UTC
f9e01c6 a working fix 27 April 2015, 00:28:28 UTC
45ea02d not going through internal contigs' blocks 25 April 2015, 22:54:31 UTC
783cbf1 fix for preferred edges heuristic 25 April 2015, 21:33:36 UTC
dc887bc reverted to the original algorithm 25 April 2015, 21:32:52 UTC
7ac914c somethiing that don't work 25 April 2015, 21:23:27 UTC
a12416b faster version 25 April 2015, 20:16:59 UTC
6c30aba fixed version 25 April 2015, 07:17:04 UTC
2f3a02f path covering algorithm 25 April 2015, 01:51:16 UTC
9f58335 guiding by previous iteration (seems to be not working though) 24 April 2015, 01:03:25 UTC
eda93fd experimental preferred edges selection 23 April 2015, 23:24:29 UTC
c487145 quick fix 23 April 2015, 21:06:05 UTC
bd67ec3 additional logging 23 April 2015, 20:49:08 UTC
6862b73 Merge branch 'devel' of https://github.com/fenderglass/Ragout into devel 23 April 2015, 20:45:44 UTC
99b58de maf2synteny updated 14 April 2015, 00:33:38 UTC
d3f213f 1.1 release 22 March 2015, 19:11:36 UTC
4bf798f chimera detection on by default 22 March 2015, 19:05:32 UTC
1b87419 no search for chimeras by default, removed debug output 20 March 2015, 03:18:59 UTC
aac094f new config paramter for chimeras 20 March 2015, 03:13:14 UTC
818acc4 merge 19 March 2015, 03:46:36 UTC
3349756 more documentation 19 March 2015, 03:39:11 UTC
f90cd91 documentation improved, moving to new release 19 March 2015, 01:31:32 UTC
a010582 non-negative tree lengths, dosumentationimproved 18 March 2015, 01:59:36 UTC
b96240c automatic synteny block scale inference 17 March 2015, 00:37:38 UTC
a2f8861 blocks sizes pre-sets instead of setting them manually 16 March 2015, 21:38:45 UTC
d7eebef Automatic tree inference 13 March 2015, 04:09:52 UTC
8b3ee82 neighbor-joining algorithm 13 March 2015, 02:59:55 UTC
54c0ed3 a step towards inferring phylogenetic tree from the data 12 March 2015, 04:08:40 UTC
bd35cb5 added extra condition in split_by_instance 05 March 2015, 20:35:08 UTC
d36d12e small fix in mergin algorithm to prevent scaffolds of length zero 04 March 2015, 22:33:27 UTC
d22c112 logging 04 March 2015, 04:02:22 UTC
f248c08 more smarter and efficient splitting by contig instance algorithm 04 March 2015, 03:59:55 UTC
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