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https://github.com/jttoivon/MODER
05 April 2024, 18:07:21 UTC
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Revision Author Date Message Commit Date
c485231 Jarkko Toivonen 31 March 2020, 18:10:18 UTC Fixed indexing bug. The list comprehensions of Python2 leak their index variables. Fixed the problem by using other index names in list comprehensions than 'i'. 31 March 2020, 18:13:54 UTC
a60d96f jttoivon 30 March 2020, 18:42:11 UTC Added a link to moder2 30 March 2020, 18:42:11 UTC
2d1df05 Jarkko Toivonen 30 March 2020, 18:37:58 UTC Got rid of deprecated argument forms 30 March 2020, 18:37:58 UTC
a236f9e Jarkko Toivonen 28 June 2018, 14:29:56 UTC Fixed issue with too long logos. Now the maximum logo length is 500. 28 June 2018, 14:29:56 UTC
d9ffbc1 Jarkko Toivonen 18 June 2018, 16:14:46 UTC There was a bug in the bug fix. 18 June 2018, 16:14:46 UTC
374b174 Jarkko Toivonen 15 June 2018, 14:46:10 UTC Fixed a bug in spaced dimer models. Bug was visible when --max-gap-learned was used. 15 June 2018, 14:50:13 UTC
5b78d43 Jarkko Toivonen 08 June 2018, 13:24:06 UTC Added support for fastq input files. 08 June 2018, 13:24:06 UTC
835bd0d Jarkko Toivonen 07 June 2018, 09:32:53 UTC Fixed a problem with dependencies. 07 June 2018, 09:32:53 UTC
f11ecc0 Jarkko Toivonen 07 June 2018, 09:23:42 UTC Fixed problem with windows line endings in input sequences. 07 June 2018, 09:26:20 UTC
cce1be3 Jarkko Toivonen 08 May 2018, 07:32:03 UTC Moder can now reverse complement the input strands. 08 May 2018, 07:32:03 UTC
2465766 Jarkko Toivonen 07 May 2018, 17:24:41 UTC Suffix array was not aware of RNA alphabet. Fixed. 07 May 2018, 17:24:41 UTC
5d6dd59 Jarkko Toivonen 07 May 2018, 16:28:54 UTC Merge branch 'rna' 07 May 2018, 16:28:54 UTC
593fa77 Jarkko Toivonen 07 May 2018, 16:28:34 UTC Finished RNA mode. 07 May 2018, 16:28:34 UTC
3afbce6 Jarkko Toivonen 07 May 2018, 11:16:31 UTC Added link to final article. 07 May 2018, 11:16:31 UTC
c2f9986 Jarkko Toivonen 07 May 2018, 08:58:20 UTC Half-way through the changes towards RNA mode. 07 May 2018, 08:58:20 UTC
50ff5aa Jarkko Toivonen 04 May 2018, 14:44:37 UTC Bumped version. 04 May 2018, 14:44:37 UTC
ccebd59 Jarkko Toivonen 04 May 2018, 14:41:23 UTC Remove out-commented code. 04 May 2018, 14:41:23 UTC
af9945b Jarkko Toivonen 04 May 2018, 14:28:49 UTC Commented out unneeded code. 04 May 2018, 14:28:49 UTC
6325d89 Jarkko Toivonen 04 May 2018, 11:30:16 UTC Small change 04 May 2018, 11:30:16 UTC
aa1f038 Jarkko Toivonen 04 May 2018, 09:27:38 UTC Merge branch 'master' into markov 04 May 2018, 09:27:38 UTC
2c665f6 Jarkko Toivonen 04 May 2018, 09:10:08 UTC Merge branch 'master' of https://github.com/jttoivon/MODER 04 May 2018, 09:10:08 UTC
cfdc48a Jarkko Toivonen 04 May 2018, 09:07:47 UTC Fixed cob table bug, when sequences are very short. 04 May 2018, 09:07:47 UTC
33aa7ee Jarkko Toivonen 27 April 2018, 07:30:02 UTC Cleaned-up code. 27 April 2018, 07:30:02 UTC
8d59e09 Jarkko Toivonen 07 March 2018, 16:21:02 UTC Removed out commented code 07 March 2018, 16:21:02 UTC
6257fd9 Jarkko Toivonen 07 March 2018, 16:07:59 UTC Fixed a buf. 07 March 2018, 16:07:59 UTC
914050e Jarkko Toivonen 07 March 2018, 15:15:55 UTC Commented away unneeded code 07 March 2018, 15:15:55 UTC
bb70716 Jarkko Toivonen 07 March 2018, 13:35:09 UTC Cleaned code up a bit 07 March 2018, 13:35:09 UTC
e935e54 Jarkko Toivonen 06 March 2018, 18:28:32 UTC Fixed a heatmap bug on OSX 06 March 2018, 18:28:32 UTC
044a593 Jarkko Toivonen 14 December 2017, 15:08:17 UTC Fixed a bug 06 March 2018, 14:38:44 UTC
28f8d97 Jarkko Toivonen 13 December 2017, 16:24:30 UTC Reorganized code a bit 06 March 2018, 14:38:44 UTC
5049b97 Jarkko Toivonen 05 March 2018, 17:06:22 UTC Small fixes. 05 March 2018, 17:06:22 UTC
8036e8f Jarkko Toivonen 15 February 2018, 17:50:52 UTC Small change 15 February 2018, 17:50:52 UTC
5c844ea Jarkko Toivonen 15 February 2018, 17:38:00 UTC Tried to improve compatibility with OSX. 15 February 2018, 17:38:00 UTC
3073201 Jarkko Toivonen 13 February 2018, 10:05:23 UTC Merge branch 'maketest' 13 February 2018, 10:05:23 UTC
883c14a Jarkko Toivonen 13 February 2018, 10:05:18 UTC Increased version number. 13 February 2018, 10:05:18 UTC
cf8874a Jarkko Toivonen 13 February 2018, 10:02:16 UTC Input can now be in fasta format. This is detected based on .fasta or .fa ending. Otherwise, sequence file is expected. 13 February 2018, 10:02:16 UTC
537f636 Jarkko Toivonen 31 January 2018, 11:09:38 UTC Improved documentation 31 January 2018, 11:09:38 UTC
b20fc56 Jarkko Toivonen 31 January 2018, 08:30:39 UTC Fixed a small bug. 31 January 2018, 08:30:39 UTC
0c1bcb6 Jarkko Toivonen 31 January 2018, 06:29:20 UTC Small improvements to the report generation 31 January 2018, 06:29:20 UTC
9c2ad3c Jarkko Toivonen 26 January 2018, 08:06:01 UTC Partial support of openmp with clang. Clang supports only a subset of features of openmp 4.0. 26 January 2018, 08:06:01 UTC
9a497d4 Jarkko Toivonen 25 January 2018, 18:36:40 UTC Tried to make moder compatible with clang. 25 January 2018, 18:36:40 UTC
a5a1087 Jarkko Toivonen 25 January 2018, 09:33:01 UTC Tried to fix dependencies between main and CPM03 modules. Also tried to fix problem with parallelization of make related to make dist. 25 January 2018, 09:33:01 UTC
5553c72 Jarkko Toivonen 22 January 2018, 21:47:10 UTC Added a missing file 22 January 2018, 21:47:10 UTC
d298888 Jarkko Toivonen 22 January 2018, 17:47:51 UTC Merge branch 'kimmo' 22 January 2018, 17:47:51 UTC
2c44f13 Jarkko Toivonen 22 January 2018, 14:39:46 UTC Fixed Makefile, removed commented code 22 January 2018, 14:39:46 UTC
4277e16 Jarkko Toivonen 19 January 2018, 13:27:23 UTC Commented out code 19 January 2018, 13:27:23 UTC
75ca7e7 Jarkko Toivonen 19 January 2018, 11:47:39 UTC Added myspacek40 19 January 2018, 11:47:39 UTC
d9a06bf Jarkko Toivonen 19 January 2018, 09:37:17 UTC Squashed commit of the following: commit 2f4b7fe941464eb4a8f6529f074e3d8c3d5257a7 Author: Jarkko Toivonen <jttoivon@cs.helsinki.fi> Date: Fri Jan 19 11:34:15 2018 +0200 Deleted a file commit e94d2e709f7eb1f900e3bc636a6ba3cca7804ab6 Author: Jarkko Toivonen <jttoivon@cs.helsinki.fi> Date: Fri Jan 19 10:43:31 2018 +0200 Improved documentation commit 75d15ae7aacbab03240cb58503a472afa802446a Author: Jarkko Toivonen <jttoivon@cs.helsinki.fi> Date: Wed Jan 17 17:27:10 2018 +0200 Included new utilities to the Makefile commit 2f85a4392611ae35d32a9168121ec96eab01e1e6 Author: Jarkko Toivonen <jttoivon@cs.helsinki.fi> Date: Wed Jan 17 16:30:39 2018 +0200 Many changes. Updated documentation. Included heatmap.py for cob visualization. Included myspacek.c for pfm visualization. Dirichlet pseudo counts is now on by default. MODER now prints -command line -hostname -start time -version number -shortest and longest line length 19 January 2018, 09:37:17 UTC
0364f0b Kimmo Palin 18 January 2018, 09:13:15 UTC Fixed documentation to fit the implementation 18 January 2018, 09:13:15 UTC
71ee787 Kimmo Palin 10 January 2018, 12:43:07 UTC Got rid of old MODER parts and now only compile the all_pairs_hudding code. 10 January 2018, 12:43:07 UTC
f8b2fef Jarkko Toivonen 09 January 2018, 09:52:14 UTC Small change 09 January 2018, 10:00:10 UTC
d3efedf Kimmo Palin 19 December 2017, 14:15:20 UTC Fast to compute. Slow to write 19 December 2017, 14:15:20 UTC
e0e2b28 Kimmo Palin 18 December 2017, 13:01:29 UTC Changed the program to just calculate pairwise huddinge distances 18 December 2017, 13:01:29 UTC
5c05124 Kimmo Palin 18 December 2017, 12:55:24 UTC Removed commented out code 18 December 2017, 12:55:24 UTC
02af2b4 Jarkko Toivonen 08 December 2017, 10:09:30 UTC Fixed Makefile dependencies. 08 December 2017, 10:09:30 UTC
2f94840 Jarkko Toivonen 08 December 2017, 09:20:46 UTC Log-scale computation used everywhere. 08 December 2017, 09:20:46 UTC
7ac7450 Jarkko Toivonen 23 November 2017, 09:19:34 UTC Complete_data_log_likelihood now uses log matrices. 23 November 2017, 09:19:34 UTC
9a0fdbc Jarkko Toivonen 22 November 2017, 14:30:09 UTC Small fix. 22 November 2017, 14:30:09 UTC
99d5a7f Jarkko Toivonen 22 November 2017, 13:00:39 UTC MODER now works with variable length sequences. 22 November 2017, 13:00:39 UTC
f2c207f Jarkko Toivonen 21 November 2017, 16:18:17 UTC Makefile now automatically creates dependencies. 21 November 2017, 16:18:17 UTC
34c89d8 Jarkko Toivonen 21 November 2017, 09:36:37 UTC FloatType is the type use for expectation computations. Bigger float type can now be used by changing the typedef of FloatType. It is currently set to long double. It is only used in the computations in the expectations part. For example the matrix parameters are still of type float. 21 November 2017, 09:36:37 UTC
7d15205 Jarkko Toivonen 15 November 2017, 15:21:23 UTC Small fix 15 November 2017, 15:21:23 UTC
6d90f52 Jarkko Toivonen 09 November 2017, 15:56:10 UTC MODER can now keep some monomer models fixed. 09 November 2017, 15:56:10 UTC
a247573 Jarkko Toivonen 25 October 2017, 09:10:16 UTC Avoid palindromes: off 25 October 2017, 09:10:16 UTC
960cb45 Jarkko Toivonen 24 October 2017, 11:34:36 UTC Enable palindrome avoidance 24 October 2017, 11:34:36 UTC
75dce7d Jarkko Toivonen 24 October 2017, 10:27:48 UTC Avoided references when using openmp 24 October 2017, 10:27:48 UTC
2d4f549 Jarkko Toivonen 19 October 2017, 10:50:41 UTC Removed an earlier change 19 October 2017, 10:50:41 UTC
87acd00 Jarkko Toivonen 19 October 2017, 09:11:22 UTC Now shows spent wall-time 19 October 2017, 09:11:22 UTC
c21457b Jarkko Toivonen 18 October 2017, 09:44:18 UTC Added avoid palindromes mechanism 18 October 2017, 09:44:18 UTC
4920e76 Jarkko Toivonen 17 October 2017, 15:47:58 UTC Improved output 17 October 2017, 15:47:58 UTC
48d38a5 Jarkko Toivonen 12 October 2017, 08:21:13 UTC Fix 12 October 2017, 08:21:13 UTC
009de90 Jarkko Toivonen 12 October 2017, 08:15:47 UTC Small changes 12 October 2017, 08:15:47 UTC
ef0631c Jarkko Toivonen 06 June 2017, 15:21:18 UTC MODER can now also compute the flanking positions of motifs. Option --flanks must be used to include these extended motif to program output. 06 June 2017, 15:21:18 UTC
3460ff6 Jarkko Toivonen 13 January 2017, 13:18:22 UTC Reformulated the README file, part II 13 January 2017, 13:18:22 UTC
53e6124 Jarkko Toivonen 13 January 2017, 13:15:30 UTC Reformulated the README file 13 January 2017, 13:15:30 UTC
e1355bb Jarkko Toivonen 13 January 2017, 13:10:08 UTC Changed filename 13 January 2017, 13:10:08 UTC
e871098 Jarkko Toivonen 13 January 2017, 12:39:10 UTC Changed default parameter 13 January 2017, 12:39:10 UTC
89f111c Jarkko Toivonen 13 January 2017, 08:57:08 UTC Changed the license in all source files. 13 January 2017, 08:57:08 UTC
8133e3c Jarkko Toivonen 04 January 2017, 14:32:50 UTC Added license to all source files 04 January 2017, 14:32:50 UTC
ce71e1c Jarkko Toivonen 04 January 2017, 14:30:50 UTC Pre-0.9.3 version 04 January 2017, 14:30:50 UTC
376bdbb Jarkko Toivonen 23 December 2016, 13:02:12 UTC Added license text to all source files for 0.9.2 23 December 2016, 13:02:12 UTC
0ce982f Jarkko Toivonen 23 December 2016, 12:12:27 UTC Pre-0.9.2 version 23 December 2016, 12:12:27 UTC
29d391b Jarkko Toivonen 24 March 2016, 10:01:18 UTC Improved documentation. 24 March 2016, 10:01:18 UTC
85c8fb3 Jarkko Toivonen 08 March 2016, 09:54:07 UTC Added TODO file 08 March 2016, 09:54:07 UTC
dbb535d Jarkko Toivonen 22 February 2016, 14:18:39 UTC Added licence text to all source files. 22 February 2016, 14:18:39 UTC
7a13237 Jarkko Toivonen 22 February 2016, 13:56:25 UTC Replaced example data to a published one. 22 February 2016, 13:56:25 UTC
50e2f15 Jarkko Toivonen 20 February 2016, 06:18:26 UTC Cleaned up Makefiles. 20 February 2016, 06:18:26 UTC
86612f1 Jarkko Toivonen 20 February 2016, 05:44:37 UTC Initial commit 20 February 2016, 05:44:37 UTC
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