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Test changes.#167

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sebschmi merged 1 commit intomainfrom
160-allow-to-disable-forward-jumps-in-rr-and-qq-tsms
May 7, 2026
Merged

Test changes.#167
sebschmi merged 1 commit intomainfrom
160-allow-to-disable-forward-jumps-in-rr-and-qq-tsms

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@sebschmi sebschmi commented May 7, 2026

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Copilot AI review requested due to automatic review settings May 7, 2026 08:04
@sebschmi sebschmi enabled auto-merge May 7, 2026 08:04
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Pull request overview

Adds new test inputs/configuration for a “no intra forward jump” scenario, plus a tiny arithmetic ordering tweak in the A* template-switch aligner.

Changes:

  • Added a new FASTA test case (twin_intra_forward_jump.fa) with a REF/QRY pair containing internal pattern changes.
  • Added a new TSA configuration (test_files/config/no_intra_forward_jump/config.tsa) that constrains jump behavior (notably RRQQOffset).
  • Minor refactor in template-switch entrance successor generation (base_cost + cost_increment).

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File Description
test_files/twin_intra_forward_jump.fa Adds a new REF/QRY sequence pair intended for exercising intra-forward-jump behavior.
test_files/config/no_intra_forward_jump/config.tsa Adds a new alignment config variant to disallow intra forward jumps via jump-cost function thresholds.
lib_tsalign/src/a_star_aligner/template_switch_distance.rs Swaps addition operand order when computing successor cost (no functional change expected).

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@sebschmi sebschmi merged commit 3056583 into main May 7, 2026
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@sebschmi sebschmi deleted the 160-allow-to-disable-forward-jumps-in-rr-and-qq-tsms branch May 7, 2026 08:07
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