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/hprcPclaiMakeBb.sh src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeBb.sh
index 626e0c86aa1..29b57485a19 100755
--- src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeBb.sh
+++ src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeBb.sh
@@ -1,46 +1,46 @@
 #!/bin/bash
-# Convert one pcLAI GRCh38-coordinate BED into a UCSC bigBed.
+# Convert one PCLAI GRCh38-coordinate BED into a UCSC bigBed.
 #
 # The source is a bed9+1: the name column packs three things
 # ("SAMPLE/hN/<window>_(PC1,PC2)") and column 10 is the source's "centroid"
 # column, the discretized ancestry of the window written as the PCA centroid of
 # that ancestry cluster (hence only four distinct values across the whole
 # release). Those are split into their own named fields (haplotype, window, pca,
 # centroid) so they can be shown on mouseover and fed to the details-page
 # scatterplot, and the name column is blanked: the
 # packed string is too long to draw as an item label and carries no extra
 # information once the fields are split out.
 #
 # thickStart/thickEnd are rewritten to the item bounds. The source format
 # specifies thickStart == chromStart and thickEnd == chromEnd; thickEnd always
 # holds, and thickStart holds except in
 # 54811 of the 11936603 windows (0.46%), where it is chromStart-1 and so outside
 # the item -- an off-by-one in the projection that bedToBigBed rejects. The two
 # columns carry no information for this annotation, so they are set to the item
 # bounds rather than dropping those windows.
 #
 # Usage: hprcPclaiMakeBb.sh <in.bed> <out.bb> <chrom.sizes>
 set -u -o pipefail
 inBed=$1; outBb=$2; sizes=$3
 SCR=$HOME/kent/src/hg/makeDb/scripts/hprcPclai
 tmp=$(mktemp "${TMPDIR:-/data/tmp}/hprcPclai.XXXXXX.bed"); trap 'rm -f "$tmp"' EXIT
 
 awk -F'\t' 'BEGIN{OFS="\t"}
   { n=split($4,a,"/");
     if (n!=3) { bad++; next }
     hap=a[1]"/"a[2]; rest=a[3];
     k=split(rest,b,"_"); pca=b[k];
     win=(pca!="") ? substr(rest,1,length(rest)-length(pca)-1) : rest;
     if ($7!=$2) fixedThick++;
     print $1,$2,$3,"",$5,$6,$7=$2,$8=$3,$9,hap,win,pca,$10 }
   END{ if (bad) print "UNPARSED_NAMES "bad" in '"$inBed"'" > "/dev/stderr";
        if (fixedThick) print "FIXED_THICKSTART "fixedThick" in '"$inBed"'" > "/dev/stderr" }' "$inBed" \
   | LC_COLLATE=C sort -k1,1 -k2,2n > "$tmp"
 
 inCount=$(wc -l < "$inBed")
 outCount=$(wc -l < "$tmp")
 [ "$inCount" = "$outCount" ] || { echo "COUNT_MISMATCH $inBed $inCount -> $outCount" >&2; exit 4; }
 
 bedToBigBed -type=bed9+4 -tab -as="$SCR/hprcPclai.as" "$tmp" "$sizes" "$outBb" \
   || { echo "BB_FAIL $inBed" >&2; exit 6; }
 echo "OK $outBb $outCount"