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CHANGELOG.md

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CHANGELOG

Unreleased changes

0.11.2

  • support for modified base energy parameter presets is available with the sc_mod_*! functions, e.g. sc_mod_pseudouridine!

  • added more ViennaRNA header files to the autogenerated Julia interface:

    • constraints/*.h (for soft/hard constraints and modified bases)

  • when building the Julia interface to the ViennaRNA headers, some patches are applied to a temporary copy of the headers before parsing with Clang.jl to fix some parsing bugs (see gen/patches-for-headers/).

0.11.0

  • update to ViennaRNA-2.6.x (from 2.5.x)

0.10.x

  • Energy parameter sets are now changed by calling functions like ViennaRNA.params_load_RNA_Turner1999() or ViennaRNA.params_load(:RNA_Turner1999) that set global variables. This more closely mirrors the ViennaRNA API and avoids the costly reloading of energy parameters inside the FoldCompound() constructor. The global variables are copied by ViennaRNA to a newly created FoldCompound when the FoldCompound() constructor is called. Previously, the kwarg param when creating a FoldCompound was used to set the parameter set.

0.9.x

  • FoldCompound: new properties max_bp_span and window_size that can be set in constructor

  • added mfe_window() to calculate mfe substructures for a sliding window

  • added mfe_window_channel() to process results from mfe_window through a Channel

  • added ViennaRNA.init_rand_seed(seedval) to seed the random number generator used by ViennaRNA

  • rename pbacktrack to sample_structures, the same name used in RNAstructure.jl and LinearFold.jl

  • sample_structures (formerly known as pbacktrack)

    • kwarg num_samples now defaults to 10 (previously: 1)
    • kwarg options must now be a Symbol, currently either :default or :nonredundant

  • plot_coords

    • restrict input types to Union{AbstractString,Pairtable}
    • new :default plot type that uses ViennaRNA's default plot type, which currently is 'puzzler'. This means the default plot type of plot_coords has changed from :simple to :puzzler

  • regenerated lib/LibRNA.jl with gen/generator.jl

    • now with ViennaRNA_jll 2.5.1 and not 2.5.0 (this was a mistake in 0.8.x, but it still worked as the differences in the headers were small)
    • always keep the version of ViennaRNA_jll used in gen/ in sync with the parent dir by using stacked pkg environments
    • include ViennaRNA mfe_window.h and part_func_window.h headers