NEWS.md

In brendanf/inferrnal: Interface to Call Programs from Infernal RNA Covariance Model Package

Changes in version 0.99.7

• Breaking change read_stockholm_msa() now returns an S4 object inheriting from class StockholmMultipleAlignment. Annotations are stored in slots of class BStringSet (GF and GC) or BStringSetList (GS and GR), allowing for annotations which do not exist for all sequences.
• read_stockholm_msa() parses GF and GS annotations split over several lines.
• Breaking change read_stockholm_msa() can parse amino acid MSA's; the "dna" argument is renamed to "type", and takes the values "RNA", "DNA", and "AA". The default is RNA, as in previous versions.
• Added writeStockholmMultipleAlignment().
• Added cmcalibrate()

Changes in version 0.99.6

• Switch to markdown for Roxygen documentation.
• Internal code reorganization.

Changes in version 0.99.5

• Correct argument "glocal" of cmalign to "global". Deprecate "glocal".
• Implement cmbuild(), along with all basic options.
• Implement all basic options for cmsearch() and cmalign().
• Add an "extra" argument to all three cm*() functions to allow passing advanced options.
• Add a "quiet" argument to suppress the sometimes very large console output of cmsearch().
• read_stockholm_msa() parses and returns residue (GR), sequence (GS), and file (GF) annotations.
• cmalign() returns an error rather than an empty alignment when Infernal exits with an error.
• If read_stockholm_msa() is given an open connection, it does not close it when done. (But if given a filename or an unopened connection, it opens and then closes.)
• cmsearch() correctly handles fields with spaces (e.g., description)

Changes in version 0.99.4

• Properly handle explicit NULL values for cpu and mxsize.

Changes in version 0.99.3

• Added mxsize argument to cmalign to change the maximum matrix size.

Changes in version 0.99.2

• Added convenience functions cm_5_8S(), sample_rRNA_fasta(), sample_rRNA_5_8S(), and sample_rRNA_stk() to access example data files.

Changes in version 0.99.1

• Added a NEWS.md file to track changes to the package.
• Added support for objects of class ShortRead as input.

brendanf/inferrnal documentation built on Feb. 4, 2023, 4:49 p.m.