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test(codec): assert the bases the codec_template consensus tests are named for - #808

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807/nhomer/test-codec-template-assert-bases
Aug 18, 2026
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nh13 merged 1 commit into
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807/nhomer/test-codec-template-assert-bases

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@nh13 nh13 commented Aug 17, 2026 •

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Closes #807.

What

Two CODEC tests added with #767 assert only the consensus length, under a codec_template doc comment that still claimed the bases were unusable and pointed at #763. #768 (the fix for #763) stores the reverse CODEC read in reference orientation, so codec_template families now consense to the reference sequence over the region the two strands share — not the mostly-N output the create_fr_pair orientation bug used to produce. This makes those tests assert the bases they are named for, and corrects the stale doc.

Changes

The two sibling codec_template tests are appropriate as-is: test_min_duplex_length_is_measured_over_the_shared_region is a threshold test and test_indel_inside_the_shared_region_is_still_rejected rejects (no bases to assert).

Verification

Each new expected literal was verified byte-for-byte against REF_BASES, not merely captured from the code:

  • dovetail (128): the body after the 2-base soft-clip edge equals REF_BASES[200..326] exactly (0 non-N mismatches, 0 Ns in the body).
  • terminal-indel (127): the body equals the reference over the shared span with the terminal deletion skipped (0 non-N mismatches); the lone N is the single-strand edge past the reverse read's close.

Test-only; no production change. cargo nextest run -p fgumi-consensus (1267 passed), cargo fmt --check, and cargo clippy -p fgumi-consensus --all-targets all clean.

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nh13 deployed to github-actions August 17, 2026 05:14 — with GitHub Actions Active
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…named for

#768 (the fix for #763) now stores the reverse CODEC read
in reference orientation, so codec_template families consense to the reference
sequence over the region the two strands share rather than the mostly-N output
the create_fr_pair orientation bug used to produce. Two #767 tests still
asserted only the consensus length, under a codec_template doc comment that
still claimed the bases were unusable and pointed at #763.

test_dovetailed_starts_without_an_indel_call_a_consensus and
test_terminal_indel_outside_the_shared_region_calls_a_consensus now assert the
emitted consensus bases, each verified byte-for-byte against REF_BASES over the
shared span (the lone N's are single-strand soft-clip read-through edges), and
the stale doc comment is corrected. The two sibling tests are threshold and
rejection tests and keep their existing assertions.

Test-only; no production change.

Closes #807.
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nh13 force-pushed the 807/nhomer/test-codec-template-assert-bases branch from cd9d13b to 0b60b38 Compare August 17, 2026 05:15
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nh13 commented Aug 17, 2026

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codecov Bot commented Aug 17, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.30%. Comparing base (257dedf) to head (0b60b38).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #808   +/-   ##
=======================================
  Coverage   94.30%   94.30%           
=======================================
  Files         186      186           
  Lines      112550   112554    +4     
=======================================
+ Hits       106136   106141    +5     
+ Misses       6414     6413    -1     

☔ View full report in Codecov by Harness.
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@nh13
nh13 merged commit 70897e2 into main Aug 18, 2026
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nh13 deleted the 807/nhomer/test-codec-template-assert-bases branch August 18, 2026 01:39
@nh13 nh13 mentioned this pull request Aug 18, 2026

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github-actions — 0b60b38c Deployed Aug 17, 2026 by nh13 via coverage #3609
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test(codec): codec_template tests assert consensus length, not bases, under a stale #763 rationale

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