ViennaRNA/ViennaRNA v2.6.0

on GitHub

Programs

• Add modified base input support to RNAfold
• Add modified base input support to RNAplfold
• Add modified base input support to RNALfold
• Add modified base input support to RNAcofold
• Add modified base input support to RNAsubopt
• Fix missing strand separators in RNAsubopt when applied to multiple interacting sequences
• Fix sorted output in RNAsubopt with --gquad option
• Allow for only -Fp in RNAinverse instead of always activating -Fm
• Fix default value of RNAinverse -R option in manpage
• Restructure --*help output and man pages for most executable programs
• Allow for cation concentration (Na+) changes in most executable programs (default 1.021M)
• Allow for at least as many threads as CPUs are configured if maximum thread number detection fails
• Fix alignment input parsing in refold.pl
• Add RNAxplorer program to the distribution

Library

• API: Extend model_details to allow for salt concentration changes
• API: Add functions for salt concentration change derived energy corrections in ViennaRNA/params/salt.h
• API: Add arbitrary modified base support (vrna_sc_mod()) via soft constraints mechanism and JSON input data
• API: Add Pseuoduridine-A parameters via soft constraints callback
• API: Add Dihydrouridine parameters via soft constraints callback
• API: Add inosine-U and inosine-C parameters via soft constraints callback
• API: Add m6A parameters via soft constraints callback mechanism
• API: Add 7DA modification support via soft constraints
• API: Add Purine (nebularine) modification support
• API: Add new soft constraints multi-callback dispatcher
• API: Add dynamic array data structure utilities
• API: Add string data structure utilities
• API: Add vrna_strchr() function
• API: Fix potential problems in free_dp_matrices() of LPfold.c
• API: Fix z-score initialization in vrna_Lfoldz() amd vrna_mfe_window_zscore_cb()
• API: Fix file close issue in vrna_file_commands_read()
• API: Fix backtracking issue in Zuker subopt
• API: Fix missing soft constraints callback execution in Zuker subopt
• API: Fix enumeration of G-quadruplexes in vrna_subopt() and vrna_subopt_cb()
• API: Fix constraints bug for exterior loop in boltzmann sampling
• API: Allow for enforcing 'must pair' constraint (|) in dot-bracket constraints strings
• API: Fix discrepancy between global and local folding in how hard constraints for unpaired bases and non-specific pairing are applied
• API: Refactor function typdefs to make them actual function pointer typedefs
• SWIG: Fix Python 3 wrapper suffix issue
• SWIG: Fix Perl 5 wrapper for vrna_ud_prob_get()
• SWIG: Only accept upper triangular part of matrix input in fc.sc_bp_add()
• SWIG: Use var_array instead of tuples for Python RNA.ptable()
• SWIG: Add Python wrapper for vrna_move_neighbor_diff()
• SWIG: Add Python docstrings generated from doxygen documentation of C-library

Package

• Update libsvm to version 3.31
• Update dlib to version 19.24
• Adapt Debian dependencies
• Fix compilation issues with RNAforester
• AUTOCONF: Fix requirement checks when SVM support is deactivated and swig is missing
• AUTOMAKE: Add auto parameters for -flto compile/link flags
• AUTOCONF: Require C++17 due to dependencies to compile DLIB
• AUTOCONF: Deactivate Python 2 bindings by default