15e1169d1ba4e318b78a89bf0e09bbc1d033d950
braney
  Mon Aug 24 13:09:18 2020 -0700
first cut at Franklin display #25405

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 8b6f888..cfd8f47 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33703,24 +33703,26 @@
 #  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
 
 #############################################################################
 
 # clinvarSub track  IN PROGRESS BRANEY 8/4/20
 mkdir /cluster/data/hg19/bed/clinvarSub
 cd /cluster/data/hg19/bed/clinvarSub
 bigBedToBed /gbdb/hg19/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2,$4}' | sort > sort.main.bed
 hgsql hg19 -Ne "select varId,clinSign from clinvarSub" | sort -n  > clinSign.txt
-join -t $'\t' sort.main.bed clinSign.txt   | uniq -c | sed 's/^ *//' | sed 's/ /\t/' | tawk '{print $3,$4,$5, $6, $7, $1}' | sort -k1,1 -k2,2n > sorted.bed
+
+join -t $'\t' sort.main.bed clinSign.txt | cut -f 2- | sort -k1,1 -k2,2n -k5,5 | tawk -f gawk   | tawk -f fawk > bigBedInput.bed
+#join -t $'\t' sort.main.bed clinSign.txt   | uniq -c | sed 's/^ *//' | sed 's/ /\t/' | tawk '{print $3,$4,$5, $6, $7, $1}' | sort -k1,1 -k2,2n > sorted.bed
 # fawk written by "hand" 
-tawk -f fawk sorted.bed > bigBedInput.bed
-bedToBigBed -tab bigBedInput.bed /cluster/data/hg19/chrom.sizes clinsub.bb
+#tawk -f fawk sorted.bed > bigBedInput.bed
+bedToBigBed -type=bed9+2 -tab bigBedInput.bed /cluster/data/hg19/chrom.sizes clinsub.bb
 ln -s `pwd`/clinsub.bb /gbdb/hg19
 
 #############################################################################
 # Trios for Genome In a Bottle - DONE 08/04/2020 ChrisL
 # see ~/kent/src/hg/makeDb/giab/make.txt