Separate costs for inter and intra TS

[sebschmi]

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[Copilot]

Pull request overview

This PR splits template-switch “offset/jump” costs into separate functions for inter-template-switches (RQ/QR) vs intra-template-switches (RR/QQ), updating both the lib_tsalign config format and the lib_ts_chainalign compatibility layer accordingly.

Changes:

• Replace single Offset cost function with RQQROffset and RRQQOffset across sample/test .tsa configs and TemplateSwitchConfig parsing/printing.
• Update tsalign runtime logic to select the appropriate offset cost function based on template-switch primary/secondary.
• Update ts-chainalign limits (TsLimits) and tests to model separate inter vs intra 12-jump ranges.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test_files/config/small/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/range/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/indel/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/experiments/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/chainalignn/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/chainalign/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
test_files/config/bench/config.tsa	Update jump-cost section to use RQQROffset and RRQQOffset.
sample_tsa_config/config.tsa	Update documented sample config to the new offset cost names.
lib_tsalign/src/error.rs	Split offset V-shape validation errors into RQ/QR vs RR/QQ variants.
lib_tsalign/src/config/io.rs	Parse/print RQQROffset and RRQQOffset instead of Offset.
lib_tsalign/src/config.rs	Replace offset_costs field with two fields + add selector method offset_costs(primary, secondary).
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs	Propagate both offset cost functions into lower-bound config generation.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch_alignment.rs	Disable both offset cost functions in the alignment lower-bound config.
lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs	Use appropriate offset cost function based on TS primary/secondary when updating entrance offsets.
lib_tsalign/src/a_star_aligner/template_switch_distance.rs	Thread both offset-cost-at-zero values into initial TS-entrance successor generation.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/template_switch_specifics.rs	Use (primary, secondary)-selected offset costs when reconstructing costs; update tests/config construction.
lib_ts_chainalign/src/exact_chaining/ts_34_jump/tests.rs	Update tests for renamed/split TsLimits 12-jump fields.
lib_ts_chainalign/src/exact_chaining/ts_12_jump/tests.rs	Update tests for renamed/split TsLimits 12-jump fields.
lib_ts_chainalign/src/costs/compat.rs	Map tsalign’s two offset cost functions to chainalign’s inter/intra 12-jump limits.
lib_ts_chainalign/src/costs.rs	Split jump_12 into inter_jump_12 and intra_jump_12 in TsLimits.
lib_ts_chainalign/src/chaining_lower_bounds/ts_jump/tests.rs	Update tests for renamed/split TsLimits 12-jump fields.

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