99856cacdbaa78c1e10650c00ee8cff19bc9c0da
braney
  Tue Oct 11 10:37:37 2022 -0700
update clinVarSub track

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 860bcc8..cd981b7 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33800,31 +33800,31 @@
             $buildDir/$db.rna.fa \
             $pre)
 
 # pslMismatchGapToBed: NM_001365372.1 gapIx 9 shifted right 74 bases, but next block size is only 38; report to NCBI
 # pslMismatchGapToBed: NM_001288811.1 gapIx 1 shifted left 6 bases, but previous block size is only 5; report to NCBI
 
 #  real    0m21.265s
 
  bedToBigBed -type=bed9+ -tab -as=$HOME/kent/src/hg/lib/txAliDiff.as $pre.bed \
         /hive/data/genomes/$db/chrom.sizes $pre.bb
 # pass1 - making usageList (180 chroms): 77 millis
 # pass2 - checking and writing primary data (27362 records, 20 fields): 234 millis
     ln -sf `pwd`/$pre.bb /gbdb/hg19/ncbiRefSeq/$pre.bb
 
 #############################################################################
-# clinvarSubLolly track  DONE BRANEY 12/14/2020
+# clinvarSubLolly track  DONE BRANEY 10/08/22
 mkdir /cluster/data/hg19/bed/clinvarSubLolly
 cd /cluster/data/hg19/bed/clinvarSubLolly
 bigBedToBed /gbdb/hg19/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort  -S 40g > sort.main.bed
 hgsql hg19 -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/hg19/chrom.sizes clinvarSubLolly.bb
 mkdir -p /gbdb/hg19/clinvarSubLolly
 ln -s `pwd`/clinvarSubLolly.bb /gbdb/hg19/clinvarSubLolly/clinvarSubLolly.bb