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UPDATE the gotchas with the PAM N rule and where it lives - #19

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emattei merged 1 commit into
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Nov 9, 2026
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emattei merged 1 commit into
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docs/pam-n-rule

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@emattei emattei commented Nov 9, 2026

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The rule that an N in a PAM pattern is satisfied by a genomic N is now
stated in three places that have to agree: base_matches, the Rust
matches_pam, and the oracle in tests/test_core_scan.py. The first two
disagreed until #18, and the oracle had encoded the Rust reading.

CLAUDE.md's list of what trips readers up is where someone would look before
changing one of them.

🤖 Generated with Claude Code

It is stated in base_matches, in the Rust matches_pam and in the oracle
that checks the scan, and the three have to agree: the first two did not
until this week. The list of what trips readers up is where someone
would look before changing one of them.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@emattei
emattei merged commit 1612867 into main Nov 9, 2026
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