Partial implementation of allowing TSMs to start and end outside of the focus region

[sebschmi]

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[Copilot]

Pull request overview

This PR introduces an (explicitly partial) implementation path toward allowing template-switch alignments (TSMs) to start and/or end outside the configured focus AlignmentRange, primarily to support inputs that are already gapped (e.g., derived from an existing alignment).

Changes:

• Adds a new Ts14OutOfRangeStrategy plus plumbing to compute and pass “additional explicit” TSM start/end coordinates derived from the original (gapped) sequences.
• Introduces new internal alignment node/edge kinds (Root, AlternativeStart, and indexed PrimaryReentry) to support multiple possible alignment starts/ends.
• Extends the configurable aligner + Python bindings to accept gap_characters so callers can treat sequences as gapped alignments while keeping range coordinates on ungapped sequences.

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tsalign/src/align/template_switch_distance_type_selectors.rs	Threads AdditionalExplicitTSMStartsAndEnds through the CLI strategy-selection pipeline and switches primary range pruning strategy.
tsalign/src/align.rs	Adds --allow-ts-14-out-of-range flag and computes AdditionalExplicitTSMStartsAndEnds from original sequences + skip characters.
test_files/config/bench/config.tsa	Updates benchmark configuration numeric parameters (offset/cost tables).
test_files/chr15_52720987_52721016.sh	Adds a repro script invoking --allow-ts-14-out-of-range.
test_files/chr15_52720987_52721016.fa	Adds a repro FASTA input pair for the new behavior.
test_files/chr11_39595337_39595347.sh	Adds another repro script (including a --no-ts run) invoking --allow-ts-14-out-of-range.
test_files/chr11_39595337_39595347.fa	Adds another repro FASTA input pair.
python_bindings/src/lib.rs	Adds gap_characters argument to Python Aligner.align() and forwards it to the Rust aligner.
lib_tsshow/src/ts_arrangement/source.rs	Updates pattern matches for the new/changed alignment types.
lib_tsshow/src/plain_text/mutlipair_alignment_renderer.rs	Updates rendering validation to account for new/changed alignment types.
lib_tsalign/src/tests.rs	Updates tests to pass new args/dynamic strategies and adjusts expected costs.
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/allow_ts_14_out_of_range.rs	New strategy helper to compute explicit TSM start/end coordinates outside the focus range.
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies.rs	Exposes the new allow_ts_14_out_of_range module.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs	Updates lower bound construction for new context args and new identifiers.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch_alignment.rs	Same as above for alignment lower bound logic.
lib_tsalign/src/a_star_aligner/template_switch_distance/identifier.rs	Adds Root + AlternativeStart identifiers and a constructor helper.
lib_tsalign/src/a_star_aligner/template_switch_distance/display.rs	Updates Display for new alignment/identifier variants.
lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs	Adds dynamic strategy + explicit start/end data to context; adds successor generation and updated target detection.
lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type.rs	Adds AlternativeStart and indexed PrimaryReentry, plus trait hooks for alternative start/end coordinates.
lib_tsalign/src/a_star_aligner/template_switch_distance.rs	Threads the new PrimaryReentry { reference_index, query_index } into successor construction.
lib_tsalign/src/a_star_aligner/gap_affine_edit_distance.rs	Implements new IAlignmentType hooks (alternative_start/end) as no-ops for non-TS alignment.
lib_tsalign/src/a_star_aligner/configurable_a_star_align.rs	Adds gap_characters filtering + ts_14_out_of_range plumbing and computes explicit starts/ends when enabled.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/template_switch_specifics.rs	Accounts for new internal alignment types when computing alignment costs.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/stream.rs	Accounts for new internal alignment types in stream coordinate logic.
lib_tsalign/src/a_star_aligner/alignment_result.rs	Extends IAlignmentType and stores alignment limits in statistics; adds alignment_range() accessor.
lib_tsalign/src/a_star_aligner/alignment_geometry.rs	Adds AlignmentRange::new(...) plus convenience setters and coordinate accessors.
lib_tsalign/src/a_star_aligner.rs	Tries to adjust reported alignment range based on alternative start/end markers.
lib_ts_chainalign/src/chain_align.rs	Updates alignment result construction to pass an AlignmentRange instead of separate offsets.
Cargo.toml	Tweaks workspace dev/release debug profile settings.

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