347d7590b576fa145bfd0d73cee612536158ed60
braney
  Wed Sep 23 11:06:11 2026 -0700
docent: rm38298 expects the reworded codon note, refs #38252 #38298

d459a7a421c changed the note from "at this codon" to "before this codon", because the
indel lies upstream of the shifted codon. The check now carries the whole new clause,
and the header makes the same correction.

Passes on genome-test. Fails at step 4 on hgwbeta (v503), which has no note.

diff --git src/hg/utils/docent/tests/regress/rm38298.docent.yaml src/hg/utils/docent/tests/regress/rm38298.docent.yaml
index e3a93adec9a..ede88a9dce1 100644
--- src/hg/utils/docent/tests/regress/rm38298.docent.yaml
+++ src/hg/utils/docent/tests/regress/rm38298.docent.yaml
@@ -1,22 +1,22 @@
 # #38298 -- the codon tooltip gave one position, and on a transcript whose sequence differs
 # from the genome the transcript position and the genomic position are not the same number.
 #
 # From MLQ #38209. On canFam3 the NCBI RefSeq tooltip for NM_001131049.1 (DNM1) at
 # chr9:55,282,762 said `Codon: c.745-747 (p.249)`, which does not agree with its own amino
 # acid label: translating c.745-747 from that transcript's CDS gives Ser, not the Arg the
-# tooltip names. The transcript has extra or missing bases against the genome at that
+# tooltip names. The transcript has extra or missing bases against the genome before that
 # codon, so the two numberings drift apart; the right transcript position is c.766-768
 # (p.256), 21 nucleotides further along.
 #
 # The fix prints BOTH, each labelled, with a note saying why they differ. So the assertion
 # is the two labelled numbers together. Either one alone would pass on a build that printed
 # only the old line, because the old line is still there under a new label.
 #
 # The codon tooltip has to be HOVERED. Unlike an exon or an item box, it is not in the
 # served map at all: the map areas of ncbiRefSeqCurated carry only `DNM1/NM_001131049.1`,
 # and the codon text is built by the page's own JavaScript when the pointer arrives. So
 # this is one `mouseover:` and three `tip:` checks on the tooltip it raises, rather than a
 # `has:` on a data-tooltip the way rm38309 reads its exon text.
 #
 # canFam3 rather than hg38 because the drift is the point and this is the case the MLQ
 # brought in. A transcript that matches the genome has one number and would not test it.
@@ -28,16 +28,19 @@
 db: canFam3
 position: chr9:55282743-55282778
 reset: true
 fast: true
 steps:
   - goto: "/cgi-bin/hgTracks?db=canFam3&position=chr9:55282743-55282778&hideTracks=1&refSeqComposite=full&ncbiRefSeqCurated=full&pix=1100"
   - expect: {rows: [ncbiRefSeqCurated]}
 
   - mouseover: {track: ncbiRefSeqCurated, at: "chr9:55282762", hold: 2}
 
   # The three claims, on the one tooltip that is now up. Both numbers, each under its own
   # label, and the sentence that says why one feature has two of them. Either number alone
   # would pass on the old build, because the old line is still there under a new label.
   - expect: {tip: "Genomic codon number: c.745-747 (p.249)"}
   - expect: {tip: "Transcript codon number: c.766-768 (p.256)"}
-  - expect: {tip: "extra or missing bases compared to the genome at this codon"}
+  # d459a7a421c (max, 2026-09-21) corrected "at this codon" to "before this codon": the indel
+  # lies upstream of the shifted codon, not in it. The check carries the whole clause so a
+  # rewording shows up here rather than half-matching.
+  - expect: {tip: "extra or missing bases compared to the genome before this codon, so the genomic and transcript codon numbers differ"}