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# clinvarSubLolly track  DONE BRANEY 10/8/2022
mkdir /cluster/data/hg38/bed/clinvarSubLolly
cd /cluster/data/hg38/bed/clinvarSubLolly
bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort  -S 40g > sort.main.bed
hgsql hg38 -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

bedToBigBed -as=$HOME/kent/src/hg/lib/clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/hg38/chrom.sizes clinvarSubLolly.bb
mkdir -p /gbdb/hg38/clinvarSubLolly
ln -s `pwd`/clinvarSubLolly.bb /gbdb/hg38/clinvarSubLolly/clinvarSubLolly.bb

bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4,$13,$15,$18,$19}' | sort  -S 40g > sort.main.bed
hgsql hg38 -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/hg38/chrom.sizes clinvarSub.bb
ln -s `pwd`/clinvarSub.bb /gbdb/hg38/clinvarSubLolly/clinvarSub.bb

