Option to force all TSM descendants to be the same.

[sebschmi]

No description provided.

[Copilot]

Pull request overview

This PR adds a configurable “descendant restriction” to the template-switch-distance A* aligner, enabling runs where all template-switch events must use the same descendant (in addition to the existing “allow any” behavior). It threads this selection through both the tsalign CLI and the lib_tsalign configurable aligner API, and introduces a DynamicStrategies parameter to the template-switch-distance alignment context.

Changes:

• Introduces a new TemplateSwitchDescendantStrategy strategy family with AllowAny and OnlyEqual implementations, and plugs it into the template-switch entrance successor generation.
• Exposes the option via tsalign CLI (--ts-descendant-strategy) and via lib_tsalign’s Aligner::set_descendant_strategy.
• Extends the template-switch-distance aligner plumbing with a DynamicStrategies context parameter and updates call sites/tests/lower-bound helpers accordingly.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tsalign/src/align/template_switch_distance_type_selectors.rs	Adds CLI selector enum and wires descendant strategy selection into the templated call chain.
tsalign/src/align.rs	Adds --ts-descendant-strategy CLI option to the main align command configuration.
test_files/twin_both_descendants.fa	Adds a new FASTA fixture likely intended for descendant-strategy testing/manual runs.
lib_tsalign/src/tests.rs	Updates template-switch-distance test invocations for the new strategy parameter(s).
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/descendant.rs	New descendant strategy implementations (AllowAny, OnlyEqualAllEqual).
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies.rs	Extends AlignmentStrategySelector / node memory to include the new descendant strategy dimension.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs	Updates lower-bound alignment strategy selection and context creation for new strategy parameter(s).
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch_alignment.rs	Same as above for the alignment lower-bound matrix codepath.
lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs	Adds DynamicStrategies to the context and reset flow.
lib_tsalign/src/a_star_aligner/template_switch_distance.rs	Enforces the descendant restriction when generating initial template-switch entrance successors.
lib_tsalign/src/a_star_aligner/configurable_a_star_align.rs	Adds descendant strategy selector, setter, and routes strategy selection into the align call.
lib_tsalign/src/a_star_aligner.rs	Extends template_switch_distance_a_star_align signature to accept/reset DynamicStrategies.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.