198 print uncertainty regions on both outer and inner sequence

[sebschmi]

No description provided.

[Copilot]

Pull request overview

Adds configurable equal-cost range (“uncertainty”) rendering for template-switch visualizations, extending the feature beyond inner sequences to optionally include outer (source) sequences, and updates workspace dependencies accordingly.

Changes:

• Replaces the boolean equal-cost-range flag with a multi-mode EqualCostRangeMode (None / InnerOnly / Full) and wires it through the rendering pipeline.
• Introduces OptionalSource characters and updates arrangement/SVG rendering so uncertainty regions can be highlighted on outer sequences in “Full” mode.
• Updates several crate dependencies (workspace-shared where appropriate) and adds a small repro test input/script.

Reviewed changes

Copilot reviewed 15 out of 16 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tsalign/src/show.rs	Switches CLI from boolean flag to EqualCostRangeMode and passes it into SvgConfig.
tsalign/Cargo.toml	Updates dependency versions (notably toml, anyhow).
test_files/twin_show_ts_optional.sh	Adds a script to generate/show an SVG demonstrating optional TS visualization.
test_files/twin_show_ts_optional.fa	Adds a small FASTA used by the new script.
lib_tsshow/src/ts_arrangement/source.rs	Adds OptionalSource and applies “Full” mode optional-marking on descendant outer sequence chars.
lib_tsshow/src/ts_arrangement/inner.rs	Gates inner equal-cost rendering on EqualCostRangeMode instead of a boolean flag.
lib_tsshow/src/ts_arrangement/index_types.rs	Updates docs to include “optional” characters in arrangement-char indexing semantics.
lib_tsshow/src/ts_arrangement/complement.rs	Treats OptionalSource similarly to Source/Hidden when building complements.
lib_tsshow/src/ts_arrangement.rs	Threads EqualCostRangeMode through arrangement construction; adds descendant helpers.
lib_tsshow/src/svg.rs	Adds EqualCostRangeMode (ValueEnum), updates legend and rendering to support optional source chars.
lib_tsshow/Cargo.toml	Updates dependencies and adds clap to support ValueEnum.
lib_tsalign/Cargo.toml	Switches thiserror to workspace dependency.
lib_ts_chainalign/Cargo.toml	Switches itertools to workspace dependency.
Cargo.toml	Bumps workspace dependency versions and adds shared itertools/thiserror.
Cargo.lock	Refreshes lockfile for the dependency updates.

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