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/hprcPclai/hprcPclaiDownload.sh src/hg/makeDb/scripts/hprcPclai/hprcPclaiDownload.sh
index b9c49e27a03..46c6dde14da 100755
--- src/hg/makeDb/scripts/hprcPclai/hprcPclaiDownload.sh
+++ src/hg/makeDb/scripts/hprcPclai/hprcPclaiDownload.sh
@@ -1,28 +1,28 @@
 #!/bin/bash
-# Download the pcLAI GRCh38-coordinate BED files for all HPRC Release 2 haplotypes.
+# Download the PCLAI GRCh38-coordinate BED files for all HPRC Release 2 haplotypes.
 # The index CSV lists one s3:// path per haplotype; s3:// is rewritten to the
 # public https endpoint of the same bucket. The submissions bucket resets
 # connections under load, so downloads are retried and run only 8-wide.
 # Usage: hprcPclaiDownload.sh <index.csv> <outDir>
 set -u -o pipefail
 idx=$1; outDir=$2
 mkdir -p "$outDir"
 
 fetchOne() {
     # args: sample haplotype s3path outDir
     local samp=$1 hap=$2 s3=$3 outDir=$4
     local out="$outDir/$samp.$hap.bed"
     [ -s "$out" ] && { echo "HAVE $samp.$hap"; return 0; }
     local url=${s3/s3:\/\/human-pangenomics\//https://s3-us-west-2.amazonaws.com/human-pangenomics/}
     curl -sfL --retry 8 --retry-delay 3 --retry-all-errors "$url" -o "$out.tmp" \
         || { echo "FAIL $samp.$hap $url" >&2; rm -f "$out.tmp"; return 1; }
     [ -s "$out.tmp" ] || { echo "EMPTY $samp.$hap $url" >&2; rm -f "$out.tmp"; return 1; }
     mv "$out.tmp" "$out"
     echo "OK $samp.$hap"
 }
 export -f fetchOne
 
 # strip the CRLF the index CSV uses, skip the header
 tail -n +2 "$idx" | tr -d '\r' \
   | awk -F, 'NF>=4 {print $1"\t"$2"\t"$4}' \
   | parallel --colsep '\t' -j 8 fetchOne {1} {2} {3} "$outDir"