c81011d4a8f57db347e15aa1248c501b2c8a6fea
lrnassar
  Mon Jun 1 13:16:15 2026 -0700
QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258

Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv,
chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the
lrSvMergeAll.py generator so a re-run reproduces it).
Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across
lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic"
and "UAE UPR").
lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1
native 161,332, each with its own type breakdown) and encode non-ASCII author
names as numeric entities.
hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231
DEL+INS, 176,531 total).
colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well
as hg38.
cpc1Sv.html: encode a Unicode minus sign as a numeric entity.

diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt
index 67d923f950d..99df493cc80 100644
--- src/hg/makeDb/doc/hg38/lrSv.txt
+++ src/hg/makeDb/doc/hg38/lrSv.txt
@@ -366,31 +366,31 @@
 # delta with a 50 bp threshold (INS, DEL, CPX, or dropped), collapses all
 # alts of one snarl ID into a single row (MIXED when types disagree),
 # and writes 16-column bed rows with AC/AN/AF and NS.
 bash ~/kent/src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh
 # hs1 bigBed: 97,205 sites (4.7 MB)
 # hg38 lifted: 81,261 sites (4.1 MB), 15,944 unmapped
 
 # Symlinks for both assemblies
 mkdir -p /gbdb/hs1/lrSv /gbdb/hg38/lrSv
 ln -sf /hive/data/genomes/hg38/bed/lrSv/cpc1/cpc1.hs1.bb  /gbdb/hs1/lrSv/cpc1.bb
 ln -sf /hive/data/genomes/hg38/bed/lrSv/cpc1/cpc1.hg38.bb /gbdb/hg38/lrSv/cpc1.bb
 
 ##########
 # 2026-04-20 Claude max
 
-# Arabic Pangenome Reference (APR) SVs
+# Arab Pangenome Reference (APR) SVs
 # Paper: Nassir et al. 2025, Nat Commun, PMID 40707445
 # Data : https://www.mbru.ac.ae/the-arab-pangenome-reference/
 #        (SharePoint download page under APR Nuclear/Pangenome)
 # Source: apr_review_v1_2902_chm13.vcf.gz (1.5 GB, 21M variants,
 # contigs named chrN with CHM13v2 lengths, multi-allelic rows).
 
 mkdir -p /hive/data/genomes/hg38/bed/lrSv/apr
 cd /hive/data/genomes/hg38/bed/lrSv/apr
 
 # (VCF placed here by the user from the MBRU SharePoint download)
 
 # Run converter + liftOver + bigBed for both hs1 (native) and hg38 (lifted).
 # The script iterates the comma-separated ALT alleles of each row,
 # classifies each by length delta (>=50 bp -> INS, <=-50 bp -> DEL,
 # |d|<50 and max(len)>=50 -> CPX, else drop), then emits one row per