32048e16a50722894cf28d9b7b4b050302e38c75
markd
  Wed Sep 30 17:54:58 2026 -0700
Spell the acronym PCLAI, not pcLAI. refs #35415

The authors write it PCLAI throughout: the upstream README at
AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title
"Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places,
across the track labels, both description pages, the makedocs, the build scripts
and the autoSql.

hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and
comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the
file was rebuilt; every line of the resulting diff differs only by the rename.

Track names, file names and the lowercase pclai in URLs and data file names are
untouched. None of them contained the string pcLAI, and renaming the tracks would
break saved sessions for no user-visible gain.

diff --git src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh
index 778ff372cf9..3a95d7be0bd 100755
--- src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh
+++ src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh
@@ -43,31 +43,31 @@
 
 # (sample,hap) -> accession, from the assemblies index
 declare -A ACC
 while IFS=$'\t' read -r s h a; do ACC["$s|$h"]="$a"; done \
   < <(tail -n +2 $IDX/asm_index.csv | awk -F, 'BEGIN{OFS="\t"}{print $1,$2,$9}')
 
 # assemblies_release2 has the two haplotype accessions SWAPPED for three samples
 # (verified: the GenArk chromAlias hprcV2 column declares the opposite hap for
 # these accessions). Correct the mapping so data is built against the assembly
 # whose sequences actually match.
 ACC["HG01978|1"]=GCA_018472865.2; ACC["HG01978|2"]=GCA_018472845.2
 ACC["HG02257|1"]=GCA_018466845.2; ACC["HG02257|2"]=GCA_018466835.2
 ACC["HG03516|1"]=GCA_018469425.2; ACC["HG03516|2"]=GCA_018469415.2
 
 # Excluded: HG002 (hg002v1.1) uses a bespoke chr-name scheme that does not match
-# its GenArk assembly's aliases (only pcLAI is present for it), and CHM13 (= hs1)
+# its GenArk assembly's aliases (only PCLAI is present for it), and CHM13 (= hs1)
 # has no annotation data here. Skip these samples.
 declare -A SKIP=( [HG002|1]=1 [HG002|2]=1 [CHM13|0]=1 )
 
 # build the job list (skip already-built outputs)
 JOBS_FILE=$WORK/jobs.txt; : > "$JOBS_FILE"
 for t in $TRACKS; do
   of=$(outfile "$t")
   tail -n +2 $IDX/idx_$t.csv | awk -F, '{print $1"\t"$2}' | sort -u \
   | while IFS=$'\t' read -r s h; do
       [ -n "${SKIP["$s|$h"]:-}" ] && continue      # excluded sample
       a=${ACC["$s|$h"]:-}
       [ -z "$a" ] && { echo "SKIP no-acc $t $s $h" >&2; continue; }
       # resume: skip only if the output is a VALID bigBed/bigWig (a killed run
       # can leave a non-empty but truncated file, which -s would accept)
       if [ "$FORCE" != 1 ] && valid "$HUB/$a/$of"; then continue; fi