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rhinotypeR News

1.7.3 (devel) — 2026-07-03

Fixed

  • Updated handling of MultipleAlignment classes for compatibility with Bioconductor 3.24 (Added MultipleAlignment to Depends to ensure compatibility with msa alignment objects).

1.7.2 (devel) — 2026-06-16

Fixed

  • Updated handling of MultipleAlignment classes for compatibility with Bioconductor 3.24.
  • Fixed alignment-related test failures under R CMD check.

1.7.1 (devel) — 2026-06-09

Fixed

  • Updated imports of DNAMultipleAlignment and related functionality following changes in Bioconductor 3.24, where multiple-alignment classes and methods were moved from Biostrings to MultipleAlignment.

1.3.1 (devel) — 2025-10-21

Fixed

  • Example and test errors related to internal helpers (compareAndColorSequences(), compute_cache()) now handled safely using \dontrun{} and updated documentation.
  • Removed outdated License stub issue and corrected DESCRIPTION metadata formatting.
  • Corrected internal tests referencing deprecated testthat::local_null_device().

Improved

  • CountSNPs() re-implementation: directly computes pairwise SNP counts without relying on model-based rounding (e.g., from MSA2dist). No rounding artifacts

1.3.0 (devel) — 2025-10-01

Added

  • New function: alignToRefs(), which aligns user sequences to the packaged rhinovirus prototype references using msa::msa() (ClustalW, ClustalOmega, or MUSCLE), with an option to trim alignments to the non-gap span of a chosen reference.

Improved

  • SNPeek() and plotAA(): now support zooming to specific genomic regions and highlighting individual sequences of interest.
  • assignTypes(): now reports the genetic distance to the nearest prototype even when the query is "unassigned".
  • Distance calculation: switched to using MSA2dist for pairwise distance computation. This provides broader model support — access to all substitution models in ape::dist.dna, in addition to the "IUPAC" model.
  • Data access: prototype and example datasets are now exported as packaged objects (rhinovirusVP4, rhinovirusPrototypesVP4) instead of being accessed via system.file(), simplifying workflows.
  • Improved documentation:
    • Improved explanations and runnable examples added where feasible.
    • Visualization functions return results invisibly to avoid console clutter, while still allowing advanced users to capture outputs.
  • Code style and formatting improved (e.g.,consistent internal helpers).

0.1.0 — Initial release

  • First public release of rhinotypeR.
  • Implements VP4/2-based rhinovirus genotyping workflow.
  • Provides bundled prototype reference sequences and example datasets.