a5c699a7301156154700f51a20ae571bc6987051
max
  Sat Sep 26 17:53:41 2026 -0700
varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424

diff --git src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfRange.sh src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfRange.sh
deleted file mode 100755
index a98baf4212e..00000000000
--- src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfRange.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-# Convert a position range of one SPARK WGS 2026_08 pVCF chunk to a sites VCF,
-# splitting the range into pieces that run in parallel on this machine.
-# Usage: sparkWgs45kPvcfRange.sh <in.vcf.gz> <groups.txt> <start> <end> <out.vcf.gz> [pieces] [jobs]
-#   start/end: 1-based, [start, end)
-# Each piece is converted by sparkWgs45kPvcfToSites.sh. Left-alignment can move
-# a record a few bases before its piece start, so the pieces are concatenated
-# and then sorted.
-set -euo pipefail
-
-inVcf=$1
-groups=$2
-start=$3
-end=$4
-outVcf=$5
-pieces=${6:-48}
-jobs=${7:-48}
-scriptDir=$(dirname "$(readlink -f "$0")")
-work=$outVcf.work
-mkdir -p "$work"
-
-step=$(( (end - start + pieces - 1) / pieces ))
-for ((i = 0; i < pieces; i++)); do
-    s=$(( start + i * step ))
-    e=$(( s + step < end ? s + step : end ))
-    [ "$s" -lt "$end" ] && printf '%s\t%d\t%d\n' "$(printf 'p%04d' $i)" "$s" "$e"
-done > "$work/pieces.txt"
-
-parallel -j "$jobs" --colsep '\t' \
-    bash "$scriptDir/sparkWgs45kPvcfToSites.sh" "$inVcf" "$groups" "$work/{1}.bcf" {2} {3} \
-    '2>' "$work/{1}.log" < "$work/pieces.txt"
-
-# Concatenate and sort the pieces
-bash "$scriptDir/sparkWgs45kPvcfMerge.sh" "$outVcf" \
-    $(cut -f1 "$work/pieces.txt" | sed "s|^|$work/|; s|$|.bcf|")
-cat "$work"/p*.log | grep -v '^Lines' || true