15bdf707a4bde0a281109bb810499a2fa98ef6ac
lrnassar
  Tue Jul 14 07:48:05 2026 -0700
Fix stale "row Y" reference in popEVE trailingFix comment per CR feedback. refs #37791

The amino acid row reorder made P the last row, not Y, but the trailingFix explanation in
the converter comment and the makedoc still said "row Y, last column". Reworded both to be
order-agnostic ("last row, last column"). Documentation only; the code already operates
positionally on labelParts[-1].

diff --git src/hg/makeDb/doc/hg38/popEve.txt src/hg/makeDb/doc/hg38/popEve.txt
index e1cd8256d86..a4d743dfb7b 100644
--- src/hg/makeDb/doc/hg38/popEve.txt
+++ src/hg/makeDb/doc/hg38/popEve.txt
@@ -48,31 +48,31 @@
 #        -> np_strand.tsv (prefer the strand on a primary chromosome)
 #   2. extract: zcat ...vcf.gz | extractPopEve.py > popEve_records.tsv
 #   3. color anchors: p0.5 / p99.5 of popEVE over all records -> anchors.txt
 #   4. sort -t$'\t' -k1,1 -k4,4n -S 4G -T sorttmp popEve_records.tsv > popEve_sorted.tsv
 #   5. vcfToPopEveHeatmap.py popEve_sorted.tsv np_strand.tsv popEve_raw.bed $LO $HI
 #   6. bedSort + awk filter to chrom.sizes -> popEve_filtered.bed
 #   7. bedToBigBed -type=bed12+ -tab -as=popEve_heatmap.as popEve_filtered.bed chrom.sizes popEve.bb
 # Scripts: ~/kent/src/hg/makeDb/scripts/popEve/{extractPopEve.py,vcfToPopEveHeatmap.py,popEve_heatmap.as}
 
 # Notes:
 #  - popEVE is distributed as genomic SNVs, so only single-nucleotide-reachable missense
 #    substitutions are scored; each heatmap column (codon) therefore has ~6-9 of 19 rows
 #    filled. This is expected and sparser than the EVE track (which scores all 19).
 #  - The heatmap renderer parses the score array (chopCommas, keeps trailing empty) and the
 #    label array (chopByCharRespectDoubleQuotesKeepEmpty, drops one trailing empty)
-#    differently. When the last cell (row Y, last column) is empty the counts disagree and
+#    differently. When the last cell (last row, last column) is empty the counts disagree and
 #    the track aborts; the converter sets a non-empty placeholder label on that one trailing
 #    cell (its score stays empty so the cell is uncolored). trailingFix count below.
 
 # Build results:
 #   records extracted: 66,400,085 (nan skipped: 15,156)
 #   color anchors: loAnchor=-5.742 hiAnchor=-2.287 (popEVE p0.5 / p99.5; median -3.358)
 #   proteins: 18,968 (18,343 distinct gene symbols; remainder are RefSeq isoforms)
 #   amino-acid positions: 10,114,809;  bases covered: 886,638,890
 #   strand: 0 inferred-vs-RefSeq mismatches; 25 proteins not in the RefSeq map (strand from
 #     coordinate inference); 0 with no strand signal; 0 dropped by chrom.sizes filter
 #   trailingFix (trailing empty cell relabeled): 15,555 proteins
 #   mouseover: HTML multi-line labels (<br>/<b>); component scores rounded to 3 dp;
 #     missing/nan components shown as NA
 #   popEve.bb size: 1,592,586,266 bytes