| a4584fb | Ronny Lorenz | 13 November 2017, 14:11:52 UTC | Prepare for release v2.4.3 | 13 November 2017, 16:42:52 UTC |
| 6c15ca8 | Ronny Lorenz | 13 November 2017, 16:42:00 UTC | TESTS: Ignore frequency of mfe structure in ensemble in RNAfold test with circular RNAs | 13 November 2017, 16:42:52 UTC |
| bf038f2 | Ronny Lorenz | 13 November 2017, 11:40:36 UTC | Prevent RNAplfold output to contain 'inf/-inf' values - This commit adds some more or less reasonable output handling for cases where the structure ensemble is emtpy due to hard constraints | 13 November 2017, 11:40:36 UTC |
| 708324a | Ronny Lorenz | 10 November 2017, 13:44:25 UTC | Merge RNAforester v2.0.1 | 10 November 2017, 13:44:25 UTC |
| e43fd3e | Ronny Lorenz | 10 November 2017, 13:44:16 UTC | Squashed 'src/RNAforester/' changes from 27994dc4..842bc9d4 842bc9d4 Bump version number to 2.0.1 44d3df5f Silence compiler warnings git-subtree-dir: src/RNAforester git-subtree-split: 842bc9d4dc99d136e83ed5015d68fc755cceb5fe | 10 November 2017, 13:44:16 UTC |
| 57b78c7 | Ronny Lorenz | 10 November 2017, 12:25:05 UTC | Merge commit 'b00b551ac969451a3de0e19ab26dc18c75357967' into development | 10 November 2017, 12:25:05 UTC |
| b00b551 | Ronny Lorenz | 10 November 2017, 12:25:05 UTC | Squashed 'src/Kinwalker/' changes from 293b820d..cd1f4c02 cd1f4c02 AUTOTOOLS: set automake to silent mode git-subtree-dir: src/Kinwalker git-subtree-split: cd1f4c021792f8174cf511e7ac8e7134b6999463 | 10 November 2017, 12:25:05 UTC |
| fee6753 | Ronny Lorenz | 08 November 2017, 15:37:00 UTC | Spellcheck CONTRIBUTING.md | 08 November 2017, 15:39:41 UTC |
| cd4a5e8 | Ronny Lorenz | 08 November 2017, 15:34:27 UTC | Add CONTRIBUTING.md | 08 November 2017, 15:34:27 UTC |
| 220634b | Ronny Lorenz | 08 November 2017, 14:49:37 UTC | Merge branch 'user-contrib' into development | 08 November 2017, 14:49:37 UTC |
| 79a82ba | Ronny Lorenz | 08 November 2017, 14:47:25 UTC | UNCRUSTIFY: part_func_up.c | 08 November 2017, 14:47:51 UTC |
| 68a615a | Ronny Lorenz | 08 November 2017, 14:44:19 UTC | Remove redundant and obsolete macros in ali_plex.c | 08 November 2017, 14:44:19 UTC |
| a53e22b | Ronny Lorenz | 08 November 2017, 14:32:25 UTC | Merge branch 'dev_circ_constraints' into 'development' Add constraint support to predictions for single circular RNA sequences See merge request !75 | 08 November 2017, 14:32:25 UTC |
| 0085624 | Ronny Lorenz | 08 November 2017, 13:23:54 UTC | Add RNAfold executable tests for circular RNAs and hard/soft constraints | 08 November 2017, 13:23:54 UTC |
| 0e52952 | Ronny Lorenz | 08 November 2017, 13:21:53 UTC | Fix soft constraint issues for unpaired nucleotides and circular RNAs | 08 November 2017, 13:21:53 UTC |
| d1ad0f3 | Martin Raden | 06 November 2017, 14:09:12 UTC | MD tweaks to get nice lists and links | 06 November 2017, 14:09:12 UTC |
| cfab928 | Ronny Lorenz | 06 November 2017, 11:39:42 UTC | Fix backtracking issues for single sequence MFE with circular RNAs - This fixes two things at once: 1. backtracking with odd dangles would always try to find multibranch loop configuration 2. hard constrained solutions with free energy above zero-line would always result in unstructured configuration, i.e. no base pairs | 06 November 2017, 11:39:42 UTC |
| 737040c | Ronny Lorenz | 25 October 2017, 21:20:30 UTC | Add generic hard/soft constraints to single-sequence circ base pair probabilities | 25 October 2017, 21:20:30 UTC |
| d5fcc16 | Ronny Lorenz | 25 October 2017, 19:54:48 UTC | Add generic hard/soft constraints to single-sequence circ partition function | 25 October 2017, 19:54:48 UTC |
| 32e08a2 | Ronny Lorenz | 24 October 2017, 17:14:19 UTC | Add generic hard/soft constraints to single-sequence circ MFE prediction | 25 October 2017, 17:18:02 UTC |
| 6ba6eac | Ronny Lorenz | 25 October 2017, 14:59:51 UTC | Fix comparative circular exterior interior loop partition function and base pair probabilities | 25 October 2017, 14:59:51 UTC |
| af3ad0b | Ronny Lorenz | 25 October 2017, 14:57:53 UTC | Fix comparative circular exterior interior loop MFE evaluation | 25 October 2017, 14:58:32 UTC |
| 3120101 | Ronny Lorenz | 25 October 2017, 14:55:06 UTC | Fix hairpin loop energy evaluation for circular case - This was mainly necessary for comparative structure prediction to avoid unusually small hairpins. | 25 October 2017, 14:55:06 UTC |
| 4b642f0 | Ronny Lorenz | 24 October 2017, 22:48:07 UTC | Fix probability computation for stochastic backtracking in RNAsubopt | 24 October 2017, 22:48:07 UTC |
| 0df29b6 | Ronny Lorenz | 20 October 2017, 21:30:59 UTC | Fix sliding-window non-specific base pair hard constraint implementation | 20 October 2017, 21:30:59 UTC |
| 0b3ca1c | Ronny Lorenz | 20 October 2017, 19:17:37 UTC | Fix sliding-window pairing probability computation with mb-loop unpaired constraint | 20 October 2017, 19:17:37 UTC |
| 0b6d5a0 | Ronny Lorenz | 20 October 2017, 12:05:38 UTC | UNCRUSTIFY: RNAplfold.c | 20 October 2017, 12:05:38 UTC |
| 4c352d4 | Ronny Lorenz | 20 October 2017, 11:38:39 UTC | Add pf_scale commandline parameter to RNAplfold | 20 October 2017, 11:43:00 UTC |
| 0cb9cd7 | Ronny Lorenz | 20 October 2017, 11:34:48 UTC | Always use sfact scaling factor in model details to compute final pf scaling factor - This stabilizes potential numerical issues for algorithms that compute partition functions but do not use an MFE prediction to estimate the magnitude of the partition function, such as RNAplfold | 20 October 2017, 11:34:48 UTC |
| d3b8815 | Ronny Lorenz | 20 October 2017, 07:11:42 UTC | Apply dangles only within sequence range in probability computation of LPfold.c | 20 October 2017, 07:11:42 UTC |
| f8094a2 | Ronny Lorenz | 20 October 2017, 07:10:29 UTC | Fix base pair hard constraints for sliding window implementations | 20 October 2017, 07:10:29 UTC |
| fa559ac | Ronny Lorenz | 18 October 2017, 13:02:33 UTC | Fix Perl5/Python2/Python3 LDFLAGS usage in corresponding Makefile.am | 18 October 2017, 13:02:33 UTC |
| ecf9260 | Ronny Lorenz | 18 October 2017, 13:02:12 UTC | UNCRUSTIFY: inverse.c | 18 October 2017, 13:02:12 UTC |
| f7eee6b | Ronny Lorenz | 18 October 2017, 12:44:36 UTC | Enclose macro block with {} in inverse.c | 18 October 2017, 13:01:42 UTC |
| 5b7b715 | Ronny Lorenz | 18 October 2017, 10:56:49 UTC | Revert "UNCRUSTIFY: inverse.[c,h]" This reverts commit 1b6aecf2b3a0ba833e3cb299d883983de0f56274. | 18 October 2017, 10:56:49 UTC |
| 351f700 | Ronny Lorenz | 17 October 2017, 12:31:17 UTC | Remove unused variable from ribo.c | 17 October 2017, 12:33:08 UTC |
| f512a67 | Ronny Lorenz | 17 October 2017, 12:30:54 UTC | remove unused variables from mfe_window.c | 17 October 2017, 12:33:07 UTC |
| 466e536 | Ronny Lorenz | 17 October 2017, 12:30:28 UTC | Remove unused variable from gquad.h | 17 October 2017, 12:33:06 UTC |
| 7c08be0 | Ronny Lorenz | 17 October 2017, 12:29:57 UTC | Remove unused variables from fold_compound.c | 17 October 2017, 12:33:06 UTC |
| f9368eb | Ronny Lorenz | 17 October 2017, 12:29:13 UTC | Fix potential use of uninitialized variable in findpath.c | 17 October 2017, 12:33:05 UTC |
| e89630f | Ronny Lorenz | 17 October 2017, 12:28:45 UTC | Remove unused variables from eval.c | 17 October 2017, 12:33:04 UTC |
| eb8502f | Ronny Lorenz | 17 October 2017, 12:27:59 UTC | Remove unused variables in alipfold.c | 17 October 2017, 12:33:03 UTC |
| cb3cee1 | Ronny Lorenz | 17 October 2017, 12:27:36 UTC | Remove unused variables in alifold.c | 17 October 2017, 12:33:03 UTC |
| c9dea3f | Ronny Lorenz | 17 October 2017, 12:26:46 UTC | Fix potential out-of-bounds memory access in RNAstruct.c | 17 October 2017, 12:33:02 UTC |
| 8dfb8cc | Ronny Lorenz | 17 October 2017, 12:25:58 UTC | Fix some potential use of uninitialized variables in ProfileDist.c/ProfileAln.c | 17 October 2017, 12:33:01 UTC |
| 682624a | Ronny Lorenz | 17 October 2017, 12:25:04 UTC | Remove unused variables from LPfold.c | 17 October 2017, 12:33:01 UTC |
| 552dbde | Ronny Lorenz | 17 October 2017, 12:32:18 UTC | UNCRUSTIFY: subopt.c | 17 October 2017, 12:33:00 UTC |
| 676a4f6 | Ronny Lorenz | 17 October 2017, 12:31:44 UTC | UNCRUSTIFY: stringdist.c | 17 October 2017, 12:32:59 UTC |
| d32f261 | Ronny Lorenz | 15 October 2017, 08:59:03 UTC | UNCRUSTIFY: utils.c | 17 October 2017, 11:33:47 UTC |
| f4263d6 | Ronny Lorenz | 15 October 2017, 08:58:32 UTC | UNCRUSTIFY: treedist.[c,h] | 17 October 2017, 11:33:47 UTC |
| 3b83e6c | Ronny Lorenz | 15 October 2017, 08:58:14 UTC | UNCRUSTIFY: svm_utils.c | 17 October 2017, 11:33:47 UTC |
| 62a0703 | Ronny Lorenz | 15 October 2017, 08:57:50 UTC | UNCRUSTIFY: snoop.[c,h] | 17 October 2017, 11:33:46 UTC |
| 1d3005b | Ronny Lorenz | 15 October 2017, 08:57:26 UTC | UNCRUSTIFY: snofold.[c,h] | 17 October 2017, 11:33:45 UTC |
| 6346c93 | Ronny Lorenz | 15 October 2017, 08:56:13 UTC | UNCRUSTIFY: ribo.[c,h] | 17 October 2017, 11:33:45 UTC |
| d6edf46 | Ronny Lorenz | 15 October 2017, 08:55:34 UTC | UNCRUSTIFY: read_epars.[c,h] | 17 October 2017, 11:33:45 UTC |
| 26492c0 | Ronny Lorenz | 15 October 2017, 08:55:08 UTC | UNCRUSTIFY: plex_functions.c | 17 October 2017, 11:33:44 UTC |
| 72db8f3 | Ronny Lorenz | 15 October 2017, 08:54:39 UTC | UNCRUSTIFY: plex.c | 17 October 2017, 11:33:44 UTC |
| 5279585 | Ronny Lorenz | 15 October 2017, 08:53:57 UTC | UNCRUSTIFY: pertubation_fold.[c,h] | 17 October 2017, 11:33:43 UTC |
| d2a020d | Ronny Lorenz | 15 October 2017, 08:53:38 UTC | UNCRUSTIFY: mm.c | 17 October 2017, 11:33:43 UTC |
| 1b6aecf | Ronny Lorenz | 15 October 2017, 08:53:14 UTC | UNCRUSTIFY: inverse.[c,h] | 17 October 2017, 11:33:43 UTC |
| 3ece5cf | Ronny Lorenz | 15 October 2017, 08:52:20 UTC | UNCRUSTIFY: findpath.[c,h] | 17 October 2017, 11:33:42 UTC |
| 782056c | Ronny Lorenz | 15 October 2017, 08:51:51 UTC | UNCRUSTIFY: duplex.[c,h] | 17 October 2017, 11:33:42 UTC |
| 9963fed | Ronny Lorenz | 15 October 2017, 08:49:47 UTC | UNCRUSTIFY: convert_epars.[c,h] | 17 October 2017, 11:33:42 UTC |
| 8273cc5 | Ronny Lorenz | 15 October 2017, 08:49:13 UTC | UNCRUSTIFY: c_plex.c | 17 October 2017, 11:33:41 UTC |
| 4255d0f | Ronny Lorenz | 15 October 2017, 08:48:15 UTC | UNCRUSTIFY: alipfold.c | 17 October 2017, 11:33:41 UTC |
| 5696a3d | Ronny Lorenz | 15 October 2017, 08:47:07 UTC | UNCRUSTIFY: alifold.c | 17 October 2017, 11:33:41 UTC |
| 3164d06 | Ronny Lorenz | 15 October 2017, 08:46:43 UTC | UNCRUSTIFY: ali_plex.[c,h] | 17 October 2017, 11:33:40 UTC |
| 26667f1 | Ronny Lorenz | 15 October 2017, 08:45:55 UTC | UNCRUSTIFY: RNAstruct.[c,h] | 17 October 2017, 11:33:40 UTC |
| eabc535 | Ronny Lorenz | 15 October 2017, 08:43:50 UTC | UNCRUSTIFY: ProfileDist.[c,h] | 17 October 2017, 11:33:39 UTC |
| ddbb50a | Ronny Lorenz | 15 October 2017, 08:43:22 UTC | UNCRUSTIFY: ProfileAln.[c,h] | 17 October 2017, 11:33:39 UTC |
| 00f7c00 | Ronny Lorenz | 15 October 2017, 08:42:49 UTC | UNCRUSTIFY: MEA.[c,h] | 17 October 2017, 11:33:39 UTC |
| 71054a3 | Ronny Lorenz | 17 October 2017, 11:31:56 UTC | REFMAN: Minor spellchecking fixes in 70-grammar.dox | 17 October 2017, 11:31:56 UTC |
| 4928f38 | Ronny Lorenz | 13 October 2017, 15:25:54 UTC | Merge tag 'v2.4.2' into development This is version 2.4.2 | 13 October 2017, 15:25:54 UTC |
| dce7f6e | Ronny Lorenz | 13 October 2017, 15:24:43 UTC | Merge tag 'v2.4.2' This is version 2.4.2 | 13 October 2017, 15:24:43 UTC |
| efd9062 | Ronny Lorenz | 12 October 2017, 15:02:54 UTC | Prepare for release 2.4.2 | 13 October 2017, 14:00:02 UTC |
| ad18470 | Ronny Lorenz | 13 October 2017, 13:54:17 UTC | Fix invalid access of pair table entry in simple_xy_coordinates | 13 October 2017, 14:00:01 UTC |
| bd7f6d6 | Ronny Lorenz | 13 October 2017, 08:37:03 UTC | Fix potential memory access errors due to invalid string copying in various executable programs - This changes the wrappers of RNA2Dfold, RNAPKplex, RNAalifold, RNAcofold, RNAfold, RNAplfold similar to what we've done before in RNAsubopt. | 13 October 2017, 08:39:32 UTC |
| 1924d5e | Ronny Lorenz | 13 October 2017, 08:35:35 UTC | Fix erroneous memory access in RNAsubopt with dot-bracket constraint | 13 October 2017, 08:39:32 UTC |
| f0fe411 | Ronny Lorenz | 13 October 2017, 07:58:26 UTC | uncrustify neighbors.c | 13 October 2017, 07:59:10 UTC |
| 59969fd | Ronny Lorenz | 13 October 2017, 07:48:48 UTC | uncrustify constraints_hard.c | 13 October 2017, 07:59:10 UTC |
| 4305ebd | Ronny Lorenz | 13 October 2017, 07:43:59 UTC | Add additional parenthesis to assignment return value check in constraints_SHAPE.c | 13 October 2017, 07:59:10 UTC |
| b5b1782 | Ronny Lorenz | 13 October 2017, 07:43:00 UTC | Add additional parenthesis to assignment return value check in file_utils.c | 13 October 2017, 07:59:10 UTC |
| ff28981 | Ronny Lorenz | 13 October 2017, 07:41:40 UTC | Fix constraint type conversion from unsigned char to char in constraints_hard.c | 13 October 2017, 07:59:09 UTC |
| c83569d | Ronny Lorenz | 13 October 2017, 07:39:52 UTC | Fix erroneous condition assignment in LPfold.c | 13 October 2017, 07:59:09 UTC |
| 6ce3d1a | Martin Mann | 05 October 2017, 09:18:40 UTC | AUTOCONF: Add compiler flag information for static-executable check which eases debugging | 12 October 2017, 14:39:31 UTC |
| f8a0714 | Ronny Lorenz | 11 October 2017, 22:22:05 UTC | TESTS: Be a bit more permissive when comparing equilibrium probabilities | 12 October 2017, 14:18:43 UTC |
| 2b7302a | Ronny Lorenz | 11 October 2017, 22:03:28 UTC | More cleanup and simplifications in constraints_hard.c - We now also introduce some more convenience macros for constraint context flags | 12 October 2017, 14:18:43 UTC |
| 2aac00d | Ronny Lorenz | 10 October 2017, 14:45:11 UTC | Some cleanup in constraints_hard.c | 12 October 2017, 14:18:43 UTC |
| f779502 | Ronny Lorenz | 02 October 2017, 18:27:53 UTC | Remove erroneous double escapes from help2man output - Actually, the problem is with gengetopt, which outputs double-escapes as is when parsing the .ggo file with --show-detailed-help option. On the other hand, the parsers in our executables do interpret the first escape properly. For instance a '\\t' in the .ggo file would result in a '\\t' in the manpage while a program output would be '\t'. To fix this sitatuation, we simply replace double escapes coming from help2man output by single escape until this is fixed in gengetopt. | 12 October 2017, 14:17:58 UTC |
| f96fe0c | Ronny Lorenz | 02 October 2017, 18:27:13 UTC | Add CSV output option to RNAcofold | 12 October 2017, 14:17:58 UTC |
| e407a5b | Gregor Entzian | 11 October 2017, 14:01:18 UTC | Implement new noLP neighbor generation | 12 October 2017, 14:02:28 UTC |
| 42b2672 | Ronny Lorenz | 11 October 2017, 21:40:18 UTC | TESTS: Minor cleanup of Perl5 and Python test script code | 11 October 2017, 21:40:18 UTC |
| 6a71abb | Ronny Lorenz | 11 October 2017, 21:38:10 UTC | TESTS: Fix Perl5 functionality check of unpaired soft constraints for sliding window MFE | 11 October 2017, 21:38:10 UTC |
| cc5b63c | Ronny Lorenz | 10 October 2017, 13:29:26 UTC | TESTS: Some cleanup in check based unit tests | 10 October 2017, 13:30:21 UTC |
| 025042e | Ronny Lorenz | 10 October 2017, 11:38:08 UTC | Do pf overflow check in equilibrium probabilities independently from hard constraints | 10 October 2017, 11:38:08 UTC |
| 1d8dcb4 | Ronny Lorenz | 10 October 2017, 11:37:03 UTC | Add missing hard constraint cases to sliding-window pf implementation | 10 October 2017, 11:37:03 UTC |
| 2be8e13 | Ronny Lorenz | 09 October 2017, 12:35:21 UTC | Fix sliding-window hard constraints where single nucleotides are prohibited from pairing | 09 October 2017, 12:35:21 UTC |
| fac1903 | Ronny Lorenz | 05 October 2017, 14:21:59 UTC | Fix sequence length confusions when input contains carriage returns - This fixes some weird issues encountered with input files tht contain carriage returns followed by newline (\r\n). Some copies of the sequence would have the carriage return removed while others didn't. We fix that by always trimming trailing special ascii characters that are usually considered 'space' or are non-printable. | 05 October 2017, 14:56:00 UTC |
| f69bf54 | Sebastian Will | 12 September 2017, 11:52:57 UTC | Fix github issue #13 | 26 September 2017, 17:49:54 UTC |
| 59c1436 | Ronny Lorenz | 26 September 2017, 17:06:45 UTC | Fix pf_scale issue in backward compatibility interface of part_func_co.c - Due to a regression, the backward compatibility interface in part_func_co.c ignores the global pf_scale variable. We fix this issue similar to what we've done to pf_fold() in commit 75a5ce1b55e5d0a561f603388ebacb71f3098d63 | 26 September 2017, 17:18:21 UTC |
