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feat: Add new wizard mode for interactive plot generation by fxwiegand · Pull Request #327 · alignoth/alignoth · GitHub

feat: Add new wizard mode for interactive plot generation - #327

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fxwiegand merged 5 commits into
mainfrom
wizard
May 26, 2025
Merged

fxwiegand merged 5 commits into
mainfrom
wizard

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This pull request introduces a new "wizard mode" to the application, enabling users to interactively generate plots through a guided CLI interface. It also includes utility enhancements and modifications to the main application logic to support this feature. Below are the most significant changes:

Wizard Mode Implementation:

  • Added a new module wizard with the wizard_mode function, which provides an interactive CLI for users to select BAM/FASTA files, specify regions, and configure plot settings. It utilizes the inquire library for prompts.
  • Integrated wizard_mode into the main function in src/main.rs, allowing the application to detect when no arguments are passed and switch to wizard mode.

Dependency Updates:

  • Added the inquire crate (version 0.7.5) to Cargo.toml to enable interactive CLI prompts.

Enhancements to Plot Output:

  • Updated the main function to save plot outputs (HTML or Vega-Lite JSON) with filenames derived from the input BAM file when using wizard mode. This ensures clear output file naming. [1] [2]

Utility Functions:

  • Introduced a new utility function get_fasta_contigs in src/utils.rs to extract contig/chromosome names from a FASTA file, which is used in wizard mode for user selection.
  • Added a unit test for get_fasta_contigs to validate its functionality.

Codebase Modifications:

  • Updated imports in src/main.rs and src/utils.rs to include the new wizard module and utility function. [1] [2]

fxwiegand merged commit 25d099e into main May 26, 2025
fxwiegand deleted the wizard branch May 26, 2025 12:16
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