https://github.com/ViennaRNA/ViennaRNA

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Revision Author Date Message Commit Date
97ffeb4 Prepare for release v2.4.9 12 July 2018, 08:56:55 UTC
a493ae4 Fix publication date in README.md 11 July 2018, 06:49:54 UTC
b399194 Slight adaptations to .gitignore files 11 July 2018, 06:49:54 UTC
dd93afc Remove Readseq related lines as it has been removed from the package some time ago 11 July 2018, 06:49:54 UTC
5d165b9 Use markdown syntax in CHANGELOG.md - And add changes to previous release up to this commit 11 July 2018, 06:49:50 UTC
5eeb2eb Rename ChangeLog to CHANGELOG.md 10 July 2018, 20:22:52 UTC
2ed711b Remove implicit exit() call for global MFE backtracking functions 10 July 2018, 20:12:02 UTC
50175d3 Warn on unsatisfiable hard constraints from dot-bracket string - The programs RNAfold and RNAcofold used to warn on unsatisfiable hard constraints, if they where read from constraints- or command files. Now, these programs and RNAalifold also raise the same warning if a provided dot-bracket string results in an empty solution space. 10 July 2018, 16:34:21 UTC
b99f885 Fix potential errors with hard constraints in MFE stack energy evaluation 10 July 2018, 16:33:19 UTC
0432034 Print correct message to quit interactive mode in RNALalifold, RNAalifold, RNAeval, and RNAplot with MSA input 10 July 2018, 12:52:50 UTC
fec433d Add short option -a as equivalent for --msa to RNAeval and RNAplot 10 July 2018, 12:52:40 UTC
7883bb5 Fix TTY batch input of multiple sequence alignments - The programs RNAalifold, RNALalifold, RNAeval, and RNAplot allow for multiple sequence alignment input (of various formats). Also, they allow for multiple alignments to run in batch mode, which works fine if input is read from file or is piped-in from stdin. In interactive mode, however, the programs stopped processing after the first alignment. As this was not the expected behavior, this is fixed now. 10 July 2018, 12:52:24 UTC
6d24045 Be more restrictive when parsing SS_cons line from Stockholm 1.0 input - Some Stockholm files seem to contain entries like #=GC SS_cons2 which also matched our checks for #=GC SS_cons. Consequently, these line where accidentally merged. We now explicitly parse only lines of the form #=GC SS_cons with at least one whitespace after the SS_cons. 10 July 2018, 12:52:14 UTC
427339a Merge branch 'user-contrib' into development 10 July 2018, 10:00:22 UTC
f0d0c60 Allow for passing dot-bracket strings with '&' strand-end identifier to simple vrna_eval_* functions 10 July 2018, 09:51:30 UTC
89c0ab7 Merge pull request #36 from martin-mann/patch-4 docu update 10 July 2018, 09:44:18 UTC
ab68c52 docu update correcting bppm switch docu in V3 API function 10 July 2018, 08:34:09 UTC
62b98f8 Add missing soft constraints to Boltzmann sampling for single RNA sequences 09 July 2018, 16:14:20 UTC
1788e78 Enable -g option for G-Quadruplex support in RNAheat 09 July 2018, 14:46:46 UTC
178c8d2 Enable verbose output for G-Quadruplex correction in comparative vrna_eval_* functions 09 July 2018, 14:34:00 UTC
6f23659 Pass-through G-Quadruplex annotation from WUSS format in vrna_db_from_WUSS() - This patch simply passes through the '++' stretches from the input WUSS format, if they are present and actually form a valid G-Quadruplex. 09 July 2018, 14:22:10 UTC
31aaf5a Update --help output for RNALalifold, RNAalifold, RNAcofold, RNAeval, RNAfold, and RNAplot 08 July 2018, 09:33:07 UTC
845a0ef Fix warning message when RNAplot is called with -j parameter but build without pthreads 07 July 2018, 21:35:56 UTC
31def9f Adapt RNAalifold, RNALalifold, and RNAplot --help output for non-wrapped aligment output 07 July 2018, 18:01:49 UTC
9920955 Allow for disabling alignment wrapping in vrna_file_PS_aln* functions 07 July 2018, 16:53:41 UTC
33712e2 Enable MSA input, multiple input files, and parallel batch processing for RNAplot - RNAplot now allows for MSA input (Stockholm 1.0 format). Besides secondary structure plots that may be color annotated by covariance of the base pairs in the consensus structure, RNAplot also allows for colored alignment EPS file output as available in RNAalifold and RNALalifold - Additionally, RNAplot now allows for multiple input files, and parallel processing of batch input 07 July 2018, 16:53:36 UTC
df10000 Adapt usage string in --help output of RNAeval 07 July 2018, 16:33:04 UTC
50780a6 Fix (position) ruler string in EPS alignment plots 07 July 2018, 16:32:19 UTC
005d2b6 Merge branch 'dev_eval_comparative' into 'development' Add MSA processing capabilities to RNAeval See merge request rna/viennarna!77 06 July 2018, 18:46:12 UTC
f7a647d Add some sequence alignment specific parameters to RNAeval - This adds parameters to change the model settings for comparative structure energy evaluation, such as covariance score weighting, ribosum scoring, etc. - This commit also adds parallel processing to RNAeval, similar to that already available with RNAfold, RNAalifold, etc. 06 July 2018, 18:38:56 UTC
99ef54c Use vrna_eval_structure_cstr() in RNAeval - Now, all RNAeval output is collected on-the-fly and printed only to stdout or whatever file stream whenever it is time to do so. 06 July 2018, 17:11:19 UTC
dd03b2b Use vrna_cstr_t for collecting output internally in eval.c - This also adds a function vrna_eval_structure_cstr() that allows for passing a vrna_cstr_t pointer that collects energy evaluation output from external programs. 06 July 2018, 17:09:35 UTC
ee9132f Add vrna_cstr_print_eval_* functions 06 July 2018, 17:08:31 UTC
a8055fe Add Stockholm input file processing capability to RNAeval - Still, MSA input for RNAeval can only be Stockholm 1.0 with SS_cons line and no SHAPE reactivity data. 06 July 2018, 15:34:53 UTC
5cfae3f Refactor RNAeval to allow for multiple input files - This is the first step towards a more flexible RNAeval that will be capable to process records from multiple files (in parallel). Also, the first steps are done to enable processing of multiple sequence alignment input. - To provide full backward compatibility, the vrna_eval_* functions need to be extended to allow for vrna_cstr_t input instead of FILE*. Otherwise, verbose output, i.e. individual loop energies per loop, are printed out-of-order with respect to the FASTA header, sequence, and dot-bracket structure string. 06 July 2018, 14:08:34 UTC
ce70b55 Include base pair soft constraints in Boltzmann sampling for single sequences 03 July 2018, 16:20:25 UTC
6f2e991 Fix wrong applicaton of base pair soft constraints for partition function computations - We usually store constraints in container-like data structures and retrieve the actual contributions just before recursion start. The function responsible to prepare base pair soft constraints for global partition function unfortunately stored the total constraints per pair using iindx, while jindx was required! 03 July 2018, 16:16:50 UTC
73257d9 Speed-up backward compatibility layer for eval_wrappers.c 03 July 2018, 14:10:31 UTC
9b12f1a Fix wrong order of function arguments for vrna_path_findpath_saddle_ub() in vrna_path_findpath_ub() - ... and speed-up backward compatibility layer for find_path.c functions 03 July 2018, 14:10:14 UTC
e1e314b Merge tag 'v2.4.8' into user-contrib This is version 2.4.8 23 June 2018, 12:54:37 UTC
1f64e87 Prepare for release of v2.4.8 23 June 2018, 11:16:10 UTC
dc44af9 Revert "Limit unpaired probability/opening energie precision to 6 digits after decimal point" This reverts commit ef00c1eb4ed84b1cc9a3aefa4784ee7944cbd35f. 22 June 2018, 20:51:35 UTC
ac45b44 Fix unpaired probability computation in LPfold.c - Internal loop contributions where not all taken into account. This mistake seems to have existed ever since version 1.8.x. Now, all internal loops up to MAXLOOP length are taken into account properly. 22 June 2018, 20:48:59 UTC
ef00c1e Limit unpaired probability/opening energie precision to 6 digits after decimal point - A precision of 7 digits sometimes produced weird 'almost 1' output for cases where the output should have been exactly 1 (and was in the internal double precision arrays). This hopefully doesn't break any pipelines that rely on unpaired probability output... 22 June 2018, 14:36:12 UTC
2882d6a Move sliding-window MFE implementation into separate object file mfe_window_wrappers.o - Otherwise, linking against libRNA.a and requiring anything from mfe_wrappers.o would pull C++ dependencies as well. Though, Link Time Optimization would probably kick that dependency out again... 22 June 2018, 11:15:32 UTC
56e5cec Merge branch 'fixRNAforester' of github.com:s-will/ViennaRNA into development 21 June 2018, 15:52:10 UTC
95041ca TESTS: Add RNAalifold special feature tests 21 June 2018, 14:51:18 UTC
64d6825 Fix several out-of-bounds access cases in eval.c 21 June 2018, 14:34:20 UTC
f938fce Fix compilation of RNAforester - RNAforester used dynamic exception specification, which are depracted since C++11 and invalid since C++17. Such specs were simply removed. - fix catch of polymorphic exception by value (should be by ref), which caused a warning, but did not have other consequences 21 June 2018, 13:31:41 UTC
afd45be Fix comparative external interior loop (circular) partition function computation - Here we actually fix two issues, one where the Boltzmann factor of the loop energy was erroneously multiplied to alignment column variable l, and a second, where loop lengths of the individual sequences in the alignment did overwrite the corresponding column-based loop length variables. 21 June 2018, 13:23:29 UTC
faf79c5 Allocate n + 2 pair table items for structure of length n - It seems, there are some parts in the library that by default access outside sequence length range at position n + 1 (and usually expect to encounter a 0 at this position). 21 June 2018, 13:17:27 UTC
b1d6019 Use memcpy() instead strcat() in io/file_formats.c io/file_formats_msa.c and io/io_utils.c 21 June 2018, 13:16:17 UTC
5c39d6c SWIG: Fix false-positive use of uninitialized value in Python3/file_py3.i 21 June 2018, 09:37:21 UTC
44d7083 CLEANUP: Removed unused variables/functions in Utils/ct2db.c 21 June 2018, 09:37:10 UTC
3b32ae5 CLEANUP: Removed unused variables/functions in RNAup.c 21 June 2018, 09:36:21 UTC
6863a8e CLEANUP: Removed unused variables/functions in RNAsubopt.c 21 June 2018, 09:36:21 UTC
c3771e2 CLEANUP: Removed unused variables/functions in RNAplot.c 21 June 2018, 09:36:21 UTC
bf49b3a CLEANUP: Removed unused variables/functions in RNAplfold.c 21 June 2018, 09:36:21 UTC
6eb1d62 CLEANUP: Removed unused variables/functions in RNApdist.c 21 June 2018, 09:36:20 UTC
830e2a9 CLEANUP: Removed unused variables/functions in RNAdistance.c 21 June 2018, 09:36:20 UTC
6f69c60 CLEANUP: Removed unused variables/functions in RNALfold.c 21 June 2018, 09:36:20 UTC
4fa4667 CLEANUP: Removed unused variables/functions in RNALalifold.c 21 June 2018, 09:36:20 UTC
a9506d5 CLEANUP: Removed unused variables/functions in plotting/probabilities.c 21 June 2018, 09:34:11 UTC
e8e20aa Fix tty input detection in RNAcofold - RNAcofold used to check whether `stdin` is an interactive terminal to decide whether or not additional output may be printed for the user. Now, we check the actual input which may be file streams as well. 20 June 2018, 16:13:15 UTC
d3c17fd TESTS: Add test case for RNAcofold -p 20 June 2018, 15:34:53 UTC
096a918 Fix free() of uninitialized values in RNAcofold with -p option - When using -p option with RNAcofold (instead of -a), some pointers to pair probability lists remain uninitialized but will be free'd. This is fixed now by assigning them an initially to NULL. 20 June 2018, 14:27:07 UTC
f3f83aa Add more shields to README.md - This simply adds some more fancy shield.io badges on top of the README.md file 19 June 2018, 22:55:54 UTC
3147447 Add Langdon 2018 RNA parameter file to distribution 13 June 2018, 20:28:44 UTC
a32778e Merge tag 'v2.4.7' into user-contrib This is version 2.4.7 13 June 2018, 20:04:16 UTC
9d7417b Merge tag 'v2.4.7' into development This is version 2.4.7 13 June 2018, 20:03:50 UTC
daf0c4f Merge tag 'v2.4.7' This is version 2.4.7 13 June 2018, 20:02:52 UTC
a4057a9 Prepare for release v2.4.7 13 June 2018, 12:54:23 UTC
6e2edcd Warn if rotational symmetry is detected in RNAcofold 13 June 2018, 12:54:23 UTC
fe8ad86 Add vrna_cstr_message_warning() function for vrna_cstr_t types 13 June 2018, 12:54:23 UTC
a775e0f SWIG: Do not link extension modules against libpython/libperl - Since our extension modules are loaded at runtime by the corresponding interpreter, we do not link them against the corresponding C libraries, i.e. libpython.so or libperl.so. The symbols of the target language libraries are present in the interpreter anyway, and, in the case of systems where the interpreter is linked statically, this would pull duplicates of the symbols at runtime (those in the shared library plus those in the statically linked interpreter) 13 June 2018, 06:07:33 UTC
3a5adc3 SWIG: Silence false positive compiler warning on possible use of undefined variable 12 June 2018, 16:45:13 UTC
641836b Silence false-positive compiler warning on use of possibly undefined variable in structure_utils.c 11 June 2018, 13:30:36 UTC
ea45268 Do not use char to access array in msa_utils.c 11 June 2018, 13:29:41 UTC
18583b6 Fix cast from char * to unsigned char * in hash_tables.c 11 June 2018, 13:25:24 UTC
b4017cb Remove implicit exit() calls from constraints/hard.c 11 June 2018, 13:05:19 UTC
1df31d0 Remove implicit exit() call in model.c 11 June 2018, 12:03:21 UTC
e27dabb Add function to check for existence of a file 11 June 2018, 10:09:40 UTC
cf4f3b5 SWIG: Add contribution note to file_py3.i 10 June 2018, 15:25:35 UTC
56db276 SWIG: Fix Python3 file stream to FILE * conversion 08 June 2018, 23:03:53 UTC
512ab85 Fix autoconf check for python3 builds - The sanity check whether we can link code against the python3 library used PYTHON3_LIBS instead of PYTHON3_LDFLAGS. Thus, library paths specified through -L... were missing, and non-standard python3 library locations were not searched for libpython3. This is fixed now, and should result in seemless builds, e.g. in Mac OSX with python3 from homebrew. 08 June 2018, 22:38:54 UTC
eb92a8f Add soft constraint callback support to subopt sensus Wuchty et al. 07 June 2018, 13:43:19 UTC
342a1e6 Add replacements for consensus(), consens_mis(), and get_ungapped_sequence() - This adds v3.0 API replacements for the above functions 07 June 2018, 12:12:22 UTC
a825201 REFMAN: Some restructuring for Secondary Structure Representationi Utilities 07 June 2018, 09:12:43 UTC
315b1e4 Add functions to replace the interface provided through RNAstruct.h - This adds replacement functions for the API in RNAstruct.h, i.e. functions to convert secondary structures to linear strings of (coarse grained) trees. - What is still missing though, is a replacement for unexpand_aligned_F() that is required in RNAdistance. 07 June 2018, 08:52:00 UTC
49fc627 Fix potential problems in multibranch loop decomposition with sliding-window MFE and soft constraints 07 June 2018, 07:26:13 UTC
5743872 Fix vrna_cstr() constructor for cases when NULL is passed as output stream 04 June 2018, 14:56:08 UTC
c7f4f3b Include src/ViennaRNA/static/ps_templates.txt in distribution tarball 04 June 2018, 12:06:36 UTC
6d0c47d Fix exclusion of SVM related interfaces when SVM support is deactivated at configure time 04 June 2018, 12:05:12 UTC
488193e SWIG: Fix header inclusion for mfe_window.i after changes in source tree 04 June 2018, 09:11:43 UTC
66e1b3a Fix leaking memory in multibranch.c 01 June 2018, 14:36:19 UTC
b569bfb Fix discrepancy between comparative and single sequence --noLP predictions - This aligns the set of allowed base pairs for comparative structure prediction with that for single sequences when using --noLP switch 31 May 2018, 11:02:42 UTC
577a861 CLEANUP: Uncrustify ct2db.c 29 May 2018, 16:33:18 UTC
f22a97a Refactor ct2db program - parser can replace unknown nucleotide characters - can read multiple structures from one file 29 May 2018, 16:22:03 UTC
1e94c1e Revert "Allow for lowercase letters in ct2db input and add some fall-through comments to make gcc happy" This reverts commit db907216261ebfb026d958d9ee8f79d336dcda67. 29 May 2018, 16:19:39 UTC
8e036d8 Changed the hash table function interface - This simply renames the functions, structs, and typedefs for the hash table implementation 29 May 2018, 14:54:16 UTC
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