Mnv handling

[qclayssen]

See sash issue

Add predefined_dbs_mbs = TRUE, for dbs type
handle mbs separately, with plot and table in case

[Copilot]

Pull Request Overview

This PR adds support for handling multi-base substitutions (MBS) alongside existing DBS/SNV/INDEL workflows and adjusts DBS handling to use predefined variant annotations. It also updates SNV plotting defaults and integrates MBS plotting and JSON export into the workflow.

• Add MBS counting, plotting, and JSON table export; integrate into sig_workflow_run
• Use predefined_dbs_mbs = TRUE when extracting DBS (and MBS) from VCF
• Update SNV rainfall default to FALSE and add logging for counting steps

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
man/sig_workflow_run.Rd	Documents workflow function; adds predefined_dbs_mbs argument description but not reflected in usage/signature.
man/sig_plot_snv.Rd	Updates function usage to include rainfall = FALSE and corrects default in docs.
man/sig_plot_mbs.Rd	Adds docs for new sig_plot_mbs; output description appears inconsistent with code (list vs single plot).
man/sig_mbs_table.Rd	Adds docs for new sig_mbs_table used for JSON export.
man/sig_count_mbs.Rd	Adds docs for new sig_count_mbs; argument list/docs inconsistent with function signature/behavior.
R/mutationalpatterns.R	Implements MBS count/plot/table; updates DBS counting to use predefined_dbs_mbs; integrates MBS into workflow and output; adds logging.
NAMESPACE	Exports new MBS-related functions.

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