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Revision Author Date Message Commit Date
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
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
cda4012 Code cleanup 02 March 2015, 03:59:07 UTC
1a5aba0 a fix in alignment function + logging 01 March 2015, 23:35:42 UTC
ae22ade couple of fixes in rr 28 February 2015, 03:03:31 UTC
1b04020 unique and repetitive matches are separated again 27 February 2015, 22:45:11 UTC
c8f031a parsimony test for repeats 27 February 2015, 07:50:36 UTC
2c43472 building profiles wrt to phylogeny 26 February 2015, 23:11:51 UTC
b9ac97a rr works more or less 26 February 2015, 20:56:34 UTC
8fdb3eb yet unfinished rr with multiple references 26 February 2015, 05:08:18 UTC
698d07c resolving repeats in non-repetitive contigs 26 February 2015, 02:37:48 UTC
0dcd958 Merge branch 'devel' into rr_devel 26 February 2015, 00:46:45 UTC
65f25fd fix for unspecified branch length + small tree parser reorganization 26 February 2015, 00:19:20 UTC
cb29f6a added 2geneorder script, tree branch scaling, void states are free to change, draft references help in chimera filtration 25 February 2015, 22:58:36 UTC
034e5a8 moving towards rr with multiple references 18 February 2015, 19:49:11 UTC
2438f90 checking for one reference 06 February 2015, 22:19:11 UTC
5ee992e oups 03 February 2015, 00:34:19 UTC
9c667ab fixed errors in merge with repeats 02 February 2015, 23:21:36 UTC
998b4d1 more conservative distance estimation 31 January 2015, 05:31:53 UTC
5169de9 fixed bug 28 January 2015, 21:51:39 UTC
659d98f oups 28 January 2015, 09:21:07 UTC
b92053a fixed distance estimation between contigs 28 January 2015, 08:43:50 UTC
c29dde6 correct version of one-ref repeat resolver 28 January 2015, 03:15:24 UTC
b28a25d moving 27 January 2015, 08:30:16 UTC
ca2df27 hangling repetitive contigs 27 January 2015, 04:09:45 UTC
d9a47f8 some changes 27 January 2015, 01:16:52 UTC
697e4f6 a fix in rr + command line option 26 January 2015, 21:50:15 UTC
d31b3b8 smarter repeats resoliving 24 January 2015, 05:03:12 UTC
8fc521b little bit more reliable prediction 19 January 2015, 21:01:47 UTC
7c89e9e --threads argument, rr disabled 19 January 2015, 20:50:24 UTC
0498a1b probably correct rr 17 January 2015, 02:36:08 UTC
1dc768d two bugfixes 17 January 2015, 01:41:16 UTC
1c57a3d rr improved a bit 16 January 2015, 03:52:51 UTC
d21ab39 an initial repeat resolver 16 January 2015, 00:58:05 UTC
ebb76de small bug in merging 15 January 2015, 20:42:29 UTC
ebd560a merging procedure handles repeats 15 January 2015, 05:07:44 UTC
9461555 more necessary refactoring 15 January 2015, 01:42:43 UTC
44f0be6 fixed error 15 January 2015, 00:13:06 UTC
7312b50 preparing to big changes 15 January 2015, 00:01:54 UTC
e508020 a possible fix for fusion prediction 12 January 2015, 22:31:37 UTC
55f7171 refactoring 12 January 2015, 22:19:06 UTC
4510624 fix in hal2fasta + conservative chimera again + fix in recipe parsing 08 January 2015, 00:13:40 UTC
ff076b8 Merge branch 'devel' of github.com:fenderglass/Ragout into devel 07 January 2015, 00:59:01 UTC
793f7cb bugfix 07 January 2015, 00:58:50 UTC
0a1595e minor fix 06 January 2015, 22:37:50 UTC
20ab4d5 fasta from hal 06 January 2015, 20:58:36 UTC
f786d0a hal backend 06 January 2015, 05:55:40 UTC
83c65dc more smart prediction 29 December 2014, 02:21:02 UTC
b8d4735 preditcion back on 28 December 2014, 08:40:02 UTC
02755e9 little bit different chimera handling 24 December 2014, 23:22:25 UTC
8956979 more precise chimera detection 23 December 2014, 07:22:30 UTC
7ebb89c bottleneck fixed 23 December 2014, 01:33:42 UTC
4a9a30e couple of small fixes 22 December 2014, 21:29:38 UTC
ee856b2 chimeras detection, some refactoring 22 December 2014, 21:12:46 UTC
fc2be5e experimental anti-fusion version 22 December 2014, 01:38:14 UTC
3dc894c joiin_collinear rewritten 18 December 2014, 02:16:09 UTC
8f9f473 nochain 11 December 2014, 23:09:49 UTC
fded228 rearrangement prediction turned off 09 December 2014, 18:56:10 UTC
209625f block parameter added 04 December 2014, 01:15:59 UTC
96c1e1e rest scripts moved to right alignmet format 04 December 2014, 01:11:43 UTC
a329583 comparison script works better, new alignment representation 04 December 2014, 00:32:46 UTC
f0f6978 more refactoring 02 December 2014, 02:56:34 UTC
5dbbb3f new version of assemblies comparison script + refactoring 02 December 2014, 02:43:34 UTC
0fc9eb6 Merge branch 'devel' of github.com:fenderglass/Ragout into devel 01 December 2014, 21:56:05 UTC
3fb655d file mode change 01 December 2014, 21:55:58 UTC
cbe8347 something changed 01 December 2014, 17:25:30 UTC
7a357f7 a script for comparing two assemblies 30 November 2014, 22:40:16 UTC
777eb5f fixed tilde recognition in config paths, tree parser now accepts float values in exp format 01 November 2014, 01:04:10 UTC
c5d640c copyright notice fo scripts 17 October 2014, 22:22:20 UTC
2a52465 added two scripts, help improved 30 September 2014, 22:07:28 UTC
4ed9f44 ambigious fasta characters 11 September 2014, 16:49:59 UTC
d599412 verification script supports both links and ord format 11 September 2014, 12:32:00 UTC
51c9f86 capturing output of native modules, logging improved 25 August 2014, 10:33:31 UTC
d919fa0 --hist option in overlap module 24 August 2014, 18:46:26 UTC
9a821fa error message fix 12 August 2014, 15:04:58 UTC
4011904 version 1.0 08 August 2014, 06:20:32 UTC
5783aa3 minor logging improvement 07 August 2014, 19:31:39 UTC
4c47ee5 refine by default, additinal testing for native modules 07 August 2014, 19:06:52 UTC
8cdb83e refinement added to tests 07 August 2014, 09:29:42 UTC
c09edca changed rows order in links file, debug output improved 07 August 2014, 09:06:56 UTC
e0a19b4 small improvement in refinement 06 August 2014, 18:23:39 UTC
5cfb484 faster cut vertex algorithm, fixed bug with debug 30 July 2014, 18:23:05 UTC
f7a3a1f more pretty links, ord removed 22 July 2014, 17:04:18 UTC
340a0ea links output format slightly changed 21 July 2014, 15:32:55 UTC
2b0ae81 Merge branch 'lanna' of github.com:fenderglass/Ragout into devel 21 July 2014, 14:45:33 UTC
94082c3 example typo 21 July 2014, 12:53:51 UTC
b924b79 Output links added 21 July 2014, 12:49:40 UTC
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