321d01255edf455466f419eb4d9dba18722068b3
jnavarr5
  Fri Aug 14 13:45:12 2026 -0700
Correct cactus447 makedoc size-check numbers to the genome-wide scan result, refs #37841

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/cactus447.txt src/hg/makeDb/doc/hg38/cactus447.txt
index e9547c4f477..014da15bf75 100644
--- src/hg/makeDb/doc/hg38/cactus447.txt
+++ src/hg/makeDb/doc/hg38/cactus447.txt
@@ -1505,31 +1505,37 @@
     # wanted, rebuild the bb with the command above.
 
     # summary bb: replicate the 2023 summary pipeline with the FIXED
     # hgLoadMafSummary. Build and run it from ~/bin/$MACHTYPE, NOT the bare name -
     # the PATH resolves to the old production binary. Script: $WORK/summary/summaryAll.sh
     # per chrom:
     #   hgLoadMafSummary -minSize=30000 -mergeGap=1500 -maxSize=200000 -test \
     #     hg38 <chrom> <chrom>.maf ; cut -f2- <chrom>.tab | sort -k1,1 -k2,2n
     # then:
     #   bedToBigBed -type=bed3+4 -as=$HOME/kent/src/hg/lib/mafSummary.as -tab \
     #     cactus447Summary.bed /hive/data/genomes/hg38/chrom.sizes cactus447waySummary.bb
     #     -> $WORK/summary/cactus447waySummary.bb
     #        1.03 GB, itemCount 74,427,201, maxDepth 446 (= 447 - hg38 reference)
 
     # VERIFICATION (all pass):
-    #   old chrY size!=nongap blocks: 94 (232 s-lines) ; new: 0
+    #   size vs non-gap base count, full scan of all 194 fix2 per-chrom MAF files
+    #     (QA 2026-08-06, refs #37841): 97,277,175 blocks, 34,527,556,943 s-lines,
+    #     0 s-lines where size != the non-gap base count, 0 where start+size runs
+    #     past srcSize. Positive control, the old (2023) chrY: 5,995 bad s-lines
+    #     out of 122,335,442. An earlier figure here, "old chrY 94 blocks
+    #     (232 s-lines)", came from a partial scan of that chrom and should not be
+    #     read as a chrY-wide count; the conclusion is unchanged.
     #   summary src column: 446 clean Genus_species names genome-wide (chrY and
     #     chr1 both), 0 with a residual dot. This is the hgLoadMafSummary
     #     name-split fix, refs #37928 (commit 2db6bab8db0, jkweb move 2070aedea88).
     #   genome bb itemCount == exact sum of the 194 per-chrom itemCounts.
 
     # STAGING (reversible; genome-test/hgwdev only - NOT pushed to public):
     #   /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/cactus447way/
     #     {hg38.cactus447way.bb, cactus447waySummary.bb, maf/} symlinked -> fix2
     #   rollback: $WORK/swap_rollback.sh
     # trackDb (human/hg38/trackDb.447way.ra, track cactus447way) already points
     # bigDataUrl/summary at hgdownload.soe.ucsc.edu; the corrected files reach the
     # live browser only after the build/QA rsync pushes fix2 to the public server.
     # frames bb (cactus447wayFrames.bb, DONE 2026-08-10): the 2023 frames were
     # built from the old blocks, so rebuilt for fix2. The per-species gene
     # predictions are gene annotations, unchanged by the re-alignment, so reuse the