0ff53d0dce4284cef2a259345eb058852d094a98
braney
  Sat Jan 6 13:07:58 2024 -0800
fix minor problem with clinvarSubLolly script that was removing the
wrong file if the --alpha flag was set

diff --git src/hg/utils/otto/clinvar/clinvarSubLolly src/hg/utils/otto/clinvar/clinvarSubLolly
index 4c12e68..1f218de 100755
--- src/hg/utils/otto/clinvar/clinvarSubLolly
+++ src/hg/utils/otto/clinvar/clinvarSubLolly
@@ -1,46 +1,46 @@
 #!/bin/bash -e
 maxDiff=$1
 dbs="hg19 hg38"
 
 if [ "$2" == "--alpha" ]; then
     alphaSuffix=Alpha
 fi
 
 for db in $dbs
 do
 workDir=subLollyBuild$db
 rm -rf $workDir
 mkdir $workDir
 cd $workDir
 bigBedToBed /gbdb/$db/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort  -S 40g > sort.main.bed
 hgsql $db -Ne "select varId,clinSign,scv from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
 
 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
 # add the line break after v409
 #tawk '{print $1":"$2 + 1"-"$3" <br>Variants (submissions):"$11}' tmp1 > tmp2
 tawk '{print $1":"$2 + 1"-"$3" Variants (submissions):"$11}' tmp1 > tmp2
 paste tmp1 tmp2 > bigBedInput.bed
 
-rm -f ../clinvarSubLolly.$db.bb
+rm -f ../clinvarSubLolly$alphaSuffix.$db.bb
 bedToBigBed -as=../clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSubLolly$alphaSuffix.$db.bb
 
 bigBedToBed /gbdb/$db/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $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
 
-rm -f ../clinvarSub.$db.bb
+rm -f ../clinvarSub$alphaSuffix.$db.bb
 bedToBigBed -as=../clinvarSubBB.as -type=bed9+11 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSub$alphaSuffix.$db.bb
 
 cd ..
 
 #validate
 
 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
 
 rm -rf $workDir
 done