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https://github.com/fenderglass/Ragout
05 April 2024, 18:02:13 UTC
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sort by:
RevisionAuthorDateMessageCommit Date
bd35cb5 Mikhail Kolmogorov05 March 2015, 20:35:08 UTCadded extra condition in split_by_instance05 March 2015, 20:35:08 UTC
d36d12e Mikhail Kolmogorov04 March 2015, 22:33:27 UTCsmall fix in mergin algorithm to prevent scaffolds of length zero04 March 2015, 22:33:27 UTC
d22c112 Mikhail Kolmogorov04 March 2015, 04:02:22 UTClogging04 March 2015, 04:02:22 UTC
f248c08 Mikhail Kolmogorov04 March 2015, 03:59:55 UTCmore smarter and efficient splitting by contig instance algorithm04 March 2015, 03:59:55 UTC
cda4012 Mikhail Kolmogorov02 March 2015, 03:59:07 UTCCode cleanup02 March 2015, 03:59:07 UTC
1a5aba0 Mikhail Kolmogorov01 March 2015, 23:35:42 UTCa fix in alignment function + logging01 March 2015, 23:35:42 UTC
ae22ade Mikhail Kolmogorov28 February 2015, 03:03:31 UTCcouple of fixes in rr28 February 2015, 03:03:31 UTC
1b04020 Mikhail Kolmogorov27 February 2015, 22:45:11 UTCunique and repetitive matches are separated again27 February 2015, 22:45:11 UTC
c8f031a Mikhail Kolmogorov27 February 2015, 07:50:36 UTCparsimony test for repeats27 February 2015, 07:50:36 UTC
2c43472 Mikhail Kolmogorov26 February 2015, 23:11:51 UTCbuilding profiles wrt to phylogeny26 February 2015, 23:11:51 UTC
b9ac97a Mikhail Kolmogorov26 February 2015, 20:56:34 UTCrr works more or less26 February 2015, 20:56:34 UTC
8fdb3eb Mikhail Kolmogorov26 February 2015, 05:08:18 UTCyet unfinished rr with multiple references26 February 2015, 05:08:18 UTC
698d07c Mikhail Kolmogorov26 February 2015, 02:37:48 UTCresolving repeats in non-repetitive contigs26 February 2015, 02:37:48 UTC
0dcd958 Mikhail Kolmogorov26 February 2015, 00:46:45 UTCMerge branch 'devel' into rr_devel26 February 2015, 00:46:45 UTC
65f25fd Mikhail Kolmogorov26 February 2015, 00:19:20 UTCfix for unspecified branch length + small tree parser reorganization26 February 2015, 00:19:20 UTC
cb29f6a Mikhail Kolmogorov25 February 2015, 22:58:36 UTCadded 2geneorder script, tree branch scaling, void states are free to change, draft references help in chimera filtration25 February 2015, 22:58:36 UTC
034e5a8 Mikhail Kolmogorov18 February 2015, 19:49:11 UTCmoving towards rr with multiple references18 February 2015, 19:49:11 UTC
2438f90 Mikhail Kolmogorov06 February 2015, 22:19:11 UTCchecking for one reference06 February 2015, 22:19:11 UTC
5ee992e Mikhail Kolmogorov03 February 2015, 00:34:19 UTCoups03 February 2015, 00:34:19 UTC
9c667ab Mikhail Kolmogorov02 February 2015, 23:21:36 UTCfixed errors in merge with repeats02 February 2015, 23:21:36 UTC
998b4d1 Mikhail Kolmogorov31 January 2015, 05:31:53 UTCmore conservative distance estimation31 January 2015, 05:31:53 UTC
5169de9 Mikhail Kolmogorov28 January 2015, 21:51:39 UTCfixed bug28 January 2015, 21:51:39 UTC
659d98f Mikahil Kolmogorov28 January 2015, 09:21:07 UTCoups28 January 2015, 09:21:07 UTC
b92053a Mikahil Kolmogorov28 January 2015, 08:43:50 UTCfixed distance estimation between contigs28 January 2015, 08:43:50 UTC
c29dde6 Mikhail Kolmogorov28 January 2015, 03:15:24 UTCcorrect version of one-ref repeat resolver28 January 2015, 03:15:24 UTC
b28a25d Mikahil Kolmogorov27 January 2015, 08:30:16 UTCmoving27 January 2015, 08:30:16 UTC
ca2df27 Mikhail Kolmogorov27 January 2015, 04:09:45 UTChangling repetitive contigs27 January 2015, 04:09:45 UTC
d9a47f8 Mikhail Kolmogorov27 January 2015, 01:16:52 UTCsome changes27 January 2015, 01:16:52 UTC
697e4f6 Mikhail Kolmogorov26 January 2015, 21:50:15 UTCa fix in rr + command line option26 January 2015, 21:50:15 UTC
d31b3b8 Mikhail Kolmogorov24 January 2015, 05:03:12 UTCsmarter repeats resoliving24 January 2015, 05:03:12 UTC
8fc521b Mikhail Kolmogorov19 January 2015, 21:01:47 UTClittle bit more reliable prediction19 January 2015, 21:01:47 UTC
7c89e9e Mikhail Kolmogorov19 January 2015, 20:50:24 UTC--threads argument, rr disabled19 January 2015, 20:50:24 UTC
0498a1b Mikhail Kolmogorov17 January 2015, 02:36:08 UTCprobably correct rr17 January 2015, 02:36:08 UTC
1dc768d Mikhail Kolmogorov17 January 2015, 01:41:16 UTCtwo bugfixes17 January 2015, 01:41:16 UTC
1c57a3d Mikhail Kolmogorov16 January 2015, 03:52:51 UTCrr improved a bit16 January 2015, 03:52:51 UTC
d21ab39 Mikhail Kolmogorov16 January 2015, 00:58:05 UTCan initial repeat resolver16 January 2015, 00:58:05 UTC
ebb76de Mikhail Kolmogorov15 January 2015, 20:42:29 UTCsmall bug in merging15 January 2015, 20:42:29 UTC
ebd560a Mikhail Kolmogorov15 January 2015, 05:07:44 UTCmerging procedure handles repeats15 January 2015, 05:07:44 UTC
9461555 Mikhail Kolmogorov15 January 2015, 01:42:43 UTCmore necessary refactoring15 January 2015, 01:42:43 UTC
44f0be6 Mikhail Kolmogorov15 January 2015, 00:13:06 UTCfixed error15 January 2015, 00:13:06 UTC
7312b50 Mikhail Kolmogorov15 January 2015, 00:01:54 UTCpreparing to big changes15 January 2015, 00:01:54 UTC
e508020 Mikhail Kolmogorov12 January 2015, 22:31:37 UTCa possible fix for fusion prediction12 January 2015, 22:31:37 UTC
55f7171 Mikhail Kolmogorov12 January 2015, 22:19:06 UTCrefactoring12 January 2015, 22:19:06 UTC
4510624 Mikhail Kolmogorov08 January 2015, 00:13:40 UTCfix in hal2fasta + conservative chimera again + fix in recipe parsing08 January 2015, 00:13:40 UTC
ff076b8 Mikhail Kolmogorov07 January 2015, 00:59:01 UTCMerge branch 'devel' of github.com:fenderglass/Ragout into devel07 January 2015, 00:59:01 UTC
793f7cb Mikhail Kolmogorov07 January 2015, 00:58:50 UTCbugfix07 January 2015, 00:58:50 UTC
0a1595e fenderglass06 January 2015, 22:37:50 UTCminor fix06 January 2015, 22:37:50 UTC
20ab4d5 Mikhail Kolmogorov06 January 2015, 20:58:36 UTCfasta from hal06 January 2015, 20:58:36 UTC
f786d0a Mikhail Kolmogorov06 January 2015, 05:55:40 UTChal backend06 January 2015, 05:55:40 UTC
83c65dc Mikhail Kolmogorov29 December 2014, 02:21:02 UTCmore smart prediction29 December 2014, 02:21:02 UTC
b8d4735 Mikhail Kolmogorov28 December 2014, 08:40:02 UTCpreditcion back on28 December 2014, 08:40:02 UTC
02755e9 Mikhail Kolmogorov24 December 2014, 23:22:25 UTClittle bit different chimera handling24 December 2014, 23:22:25 UTC
8956979 Mikhail Kolmogorov23 December 2014, 07:22:30 UTCmore precise chimera detection23 December 2014, 07:22:30 UTC
7ebb89c Mikhail Kolmogorov23 December 2014, 01:33:42 UTCbottleneck fixed23 December 2014, 01:33:42 UTC
4a9a30e Mikhail Kolmogorov22 December 2014, 21:29:38 UTCcouple of small fixes22 December 2014, 21:29:38 UTC
ee856b2 Mikhail Kolmogorov22 December 2014, 21:12:46 UTCchimeras detection, some refactoring22 December 2014, 21:12:46 UTC
fc2be5e Mikhail Kolmogorov22 December 2014, 01:38:14 UTCexperimental anti-fusion version22 December 2014, 01:38:14 UTC
3dc894c Mikhail Kolmogorov18 December 2014, 02:16:09 UTCjoiin_collinear rewritten18 December 2014, 02:16:09 UTC
8f9f473 Mikhail Kolmogorov11 December 2014, 23:09:49 UTCnochain11 December 2014, 23:09:49 UTC
fded228 Mikhail Kolmogorov09 December 2014, 18:56:10 UTCrearrangement prediction turned off09 December 2014, 18:56:10 UTC
209625f Mikhail Kolmogorov04 December 2014, 01:15:59 UTCblock parameter added04 December 2014, 01:15:59 UTC
96c1e1e Mikhail Kolmogorov04 December 2014, 01:11:43 UTCrest scripts moved to right alignmet format04 December 2014, 01:11:43 UTC
a329583 Mikhail Kolmogorov04 December 2014, 00:32:46 UTCcomparison script works better, new alignment representation04 December 2014, 00:32:46 UTC
f0f6978 Mikhail Kolmogorov02 December 2014, 02:56:34 UTCmore refactoring02 December 2014, 02:56:34 UTC
5dbbb3f Mikhail Kolmogorov02 December 2014, 02:43:34 UTCnew version of assemblies comparison script + refactoring02 December 2014, 02:43:34 UTC
0fc9eb6 Mikhail Kolmogorov01 December 2014, 21:56:05 UTCMerge branch 'devel' of github.com:fenderglass/Ragout into devel01 December 2014, 21:56:05 UTC
3fb655d Mikhail Kolmogorov01 December 2014, 21:55:58 UTCfile mode change01 December 2014, 21:55:58 UTC
cbe8347 Mikhail Kolmogorov01 December 2014, 17:25:30 UTCsomething changed01 December 2014, 17:25:30 UTC
7a357f7 Mikhail Kolmogorov30 November 2014, 22:40:16 UTCa script for comparing two assemblies30 November 2014, 22:40:16 UTC
777eb5f fenderglass01 November 2014, 01:04:10 UTCfixed tilde recognition in config paths, tree parser now accepts float values in exp format01 November 2014, 01:04:10 UTC
c5d640c fenderglass17 October 2014, 22:22:20 UTCcopyright notice fo scripts17 October 2014, 22:22:20 UTC
2a52465 fenderglass30 September 2014, 22:07:28 UTCadded two scripts, help improved30 September 2014, 22:07:28 UTC
4ed9f44 fenderglass11 September 2014, 16:49:59 UTCambigious fasta characters11 September 2014, 16:49:59 UTC
d599412 fenderglass11 September 2014, 12:32:00 UTCverification script supports both links and ord format11 September 2014, 12:32:00 UTC
51c9f86 fenderglass25 August 2014, 10:33:31 UTCcapturing output of native modules, logging improved25 August 2014, 10:33:31 UTC
d919fa0 fenderglass24 August 2014, 18:46:26 UTC--hist option in overlap module24 August 2014, 18:46:26 UTC
9a821fa fenderglass12 August 2014, 15:04:58 UTCerror message fix12 August 2014, 15:04:58 UTC
4011904 fenderglass08 August 2014, 06:20:32 UTCversion 1.008 August 2014, 06:20:32 UTC
5783aa3 fenderglass07 August 2014, 19:31:39 UTCminor logging improvement07 August 2014, 19:31:39 UTC
4c47ee5 fenderglass07 August 2014, 19:06:52 UTCrefine by default, additinal testing for native modules07 August 2014, 19:06:52 UTC
8cdb83e fenderglass07 August 2014, 09:29:42 UTCrefinement added to tests07 August 2014, 09:29:42 UTC
c09edca fenderglass07 August 2014, 09:06:56 UTCchanged rows order in links file, debug output improved07 August 2014, 09:06:56 UTC
e0a19b4 fenderglass06 August 2014, 18:23:39 UTCsmall improvement in refinement06 August 2014, 18:23:39 UTC
5cfb484 fenderglass30 July 2014, 18:23:05 UTCfaster cut vertex algorithm, fixed bug with debug30 July 2014, 18:23:05 UTC
f7a3a1f fenderglass22 July 2014, 17:04:18 UTCmore pretty links, ord removed22 July 2014, 17:04:18 UTC
340a0ea fenderglass21 July 2014, 15:32:55 UTClinks output format slightly changed21 July 2014, 15:32:55 UTC
2b0ae81 fenderglass21 July 2014, 14:45:33 UTCMerge branch 'lanna' of github.com:fenderglass/Ragout into devel21 July 2014, 14:45:33 UTC
94082c3 fenderglass21 July 2014, 12:53:51 UTCexample typo21 July 2014, 12:53:51 UTC
b924b79 Anna Lioznova21 July 2014, 12:49:40 UTCOutput links added21 July 2014, 12:49:40 UTC
7b354df fenderglass21 July 2014, 12:39:25 UTCsmall fix21 July 2014, 12:39:25 UTC
6c6048b fenderglass21 July 2014, 12:03:03 UTCImproved manual21 July 2014, 12:03:03 UTC
e59caf7 fenderglass21 July 2014, 09:46:41 UTCMerge branch 'master' into devel21 July 2014, 09:46:41 UTC
480a94c fenderglass18 July 2014, 18:59:24 UTCadded colored graph18 July 2014, 18:59:24 UTC
5bc5199 fenderglass18 July 2014, 18:35:36 UTCremoving red edges after scoring18 July 2014, 18:35:36 UTC
d01e7c7 fenderglass17 July 2014, 19:32:40 UTCanother one17 July 2014, 19:32:40 UTC
f612984 fenderglass17 July 2014, 19:28:00 UTCsmall manual fix17 July 2014, 19:28:00 UTC
65ade75 fenderglass08 July 2014, 10:52:02 UTCMerge branch 'master' into devel08 July 2014, 10:52:02 UTC
943c9e6 fenderglass08 July 2014, 10:50:54 UTCfixed example08 July 2014, 10:50:54 UTC
1ab7d18 fenderglass05 July 2014, 10:40:47 UTCMerge branch 'devel'05 July 2014, 10:40:47 UTC
0994508 fenderglass22 June 2014, 00:29:06 UTCmakefile fix for mac22 June 2014, 00:29:06 UTC
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