66d4db32ebb42c4b5005e6c39a733bc1b75457d0
max
  Mon Dec 8 08:06:52 2025 -0800
fixing clinvar bigbed type bug, refs #36810

diff --git src/hg/utils/otto/clinvar/clinvarSubLolly src/hg/utils/otto/clinvar/clinvarSubLolly
index 7117c1ff0ec..41d50f3e37e 100755
--- src/hg/utils/otto/clinvar/clinvarSubLolly
+++ src/hg/utils/otto/clinvar/clinvarSubLolly
@@ -19,32 +19,32 @@
 join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,$6,$1, $7}' | sort -S 40g -k1,1 -k2,2n -k5,5 | tawk -f ../makeFranklin   | tawk -f ../assignColors > tmp1
 tawk '{print $1":"$2 + 1"-"$3" <br>Variants (submissions):"$11}' tmp1 > tmp2
 paste tmp1 tmp2 > bigBedInput.bed
 
 bedToBigBed -as=../clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSubLolly$alphaSuffix.$db.new.bb
 
 bigBedToBed /gbdb/$db/bbi/clinvar$alphaSuffix/clinvarMain.bb stdout | tawk '{print $46, $1,$2,$2+1,$4,$13,$15,$18,$19}' | sort  -S 40g > sort.main.bed
 hgsql $db -Ne "select * from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
 join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,0,"+",0,0,"0,0,0",$6,$20,$8, $9,$1,$10,$7,$11,$12,$13,$14,$15,$16,$17,$18,$19,$21}' | sort -S 40g -k1,1 -k2,2n | tawk -f ../assignScore > bigBedInput.bed
 
 bedToBigBed -as=../clinvarSubBB.as -type=bed9+11 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSub$alphaSuffix.$db.new.bb
 
 cd ..
 
 #validate
-bigBedMaxPercDiff 5 clinvarSubLolly$alphaSuffix.$db.new.bb clinvarSubLolly$alphaSuffix.$db.bb
-bigBedMaxPercDiff 5 clinvarSub$alphaSuffix.$db.new.bb clinvarSub$alphaSuffix.$db.bb
+bigBedMaxPercDiff $maxDiff clinvarSubLolly$alphaSuffix.$db.new.bb clinvarSubLolly$alphaSuffix.$db.bb
+bigBedMaxPercDiff $maxDiff clinvarSub$alphaSuffix.$db.new.bb clinvarSub$alphaSuffix.$db.bb
 
 mv -f clinvarSub$alphaSuffix.$db.new.bb clinvarSub$alphaSuffix.$db.bb
 mv -f clinvarSubLolly$alphaSuffix.$db.new.bb clinvarSubLolly$alphaSuffix.$db.bb
 
 mkdir -p /gbdb/$db/clinvarSubLolly$alphaSuffix
 rm -f /gbdb/$db/clinvarSubLolly$alphaSuffix/clinvarSubLolly.bb /gbdb/$db/clinvarSubLolly$alphaSuffix/clinvarSub.bb
 ln -s `pwd`/clinvarSubLolly$alphaSuffix.$db.bb /gbdb/$db/clinvarSubLolly$alphaSuffix/clinvarSubLolly.bb
 ln -s `pwd`/clinvarSub$alphaSuffix.$db.bb /gbdb/$db/clinvarSubLolly$alphaSuffix/clinvarSub.bb
 
 # archive only if not in alpha mode
 if [ -z "$alphaSuffix" ]; then
     today=$(date +%F)
     cp clinvarSubLolly$alphaSuffix.$db.bb clinvarSub$alphaSuffix.$db.bb /usr/local/apache/htdocs-hgdownload/goldenPath/archive/hg38/clinvar/${today}/
 fi