Support base-cost per ts_kind in tschainalign.

[sebschmi]

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[Copilot]

Pull request overview

This PR extends lib_ts_chainalign to support a template-switch base cost that varies by TsKind (TS11/TS12/TS21/TS22), and updates chaining/exact-chaining logic and tests to use the per-kind cost.

Changes:

• Introduces TsBaseCost<Cost> and replaces AlignmentCosts.ts_base_cost: Cost with TsBaseCost<Cost>.
• Updates exact-chaining (TS12 jump) and chaining cost-function logic to apply ts_base_cost.get(ts_kind) where the TsKind is known.
• Updates compatibility conversion from lib_tsalign configs and adjusts lower-bound computations/tests accordingly.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
lib_ts_chainalign/src/exact_chaining/ts_34_jump/tests.rs	Updates tests to construct ts_base_cost via Into<TsBaseCost<_>>.
lib_ts_chainalign/src/exact_chaining/ts_12_jump/tests.rs	Updates tests to construct ts_base_cost via Into<TsBaseCost<_>>.
lib_ts_chainalign/src/exact_chaining/ts_12_jump/algo.rs	Applies ts_base_cost based on the end coordinate’s TsKind.
lib_ts_chainalign/src/costs/compat.rs	Converts lib_tsalign base-cost fields into a per-TsKind TsBaseCost.
lib_ts_chainalign/src/costs.rs	Adds TsBaseCost type and updates AlignmentCosts to use it.
lib_ts_chainalign/src/chaining_lower_bounds/ts_jump/tests.rs	Updates tests for new TsBaseCost API and uses min() where needed.
lib_ts_chainalign/src/chaining_lower_bounds/ts_jump.rs	Incorporates the base cost into 12-jump lower bounds using TsBaseCost::min().
lib_ts_chainalign/src/chaining_cost_function/tests.rs	Updates test construction of AlignmentCosts::new to pass a TsBaseCost.
lib_ts_chainalign/src/chaining_cost_function.rs	Uses ts_base_cost.get(ts_kind) when comparing against thresholds / cost limits.
lib_ts_chainalign/src/alignment/ts_kind.rs	Adds clarifying doc comments for TS11/TS12/TS21/TS22.

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