675293a87172d440c9c78b1c1bdc54610bc35a77
braney
  Tue May 7 14:14:26 2024 -0700
changes to HPRC rearrangements track in response to SAB  refs #33484

diff --git src/hg/makeDb/doc/hg38/hprcRearrange.txt src/hg/makeDb/doc/hg38/hprcRearrange.txt
index 88b02ab..8f8c75e 100644
--- src/hg/makeDb/doc/hg38/hprcRearrange.txt
+++ src/hg/makeDb/doc/hg38/hprcRearrange.txt
@@ -1,58 +1,58 @@
 # 2023-08-12 braney
 
 VERSION=V1
 inversion=hprcArrInv$VERSION
 duplication=hprcArrDup$VERSION
 all=hprcArrAll$VERSION
 
 mkdir -p /cluster/data/hg38/bed/hprc/rearrange
 cd /cluster/data/hg38/bed/hprc/rearrange
 
 # grab the chains
 ls ../chain/*.chain > chain.lst
 
 rm -rf inversions duplications
 mkdir inversions duplications
 
 # make the job that will figure out the inversions and duplications in each assembly
 while read chain 
 do
 name=`basename $chain | sed 's?.*chainHprc??' | sed 's/\.chain//'`
 echo chainArrange $chain $name inversions/$name.txt duplications/$name.txt
 done < chain.lst > jobs
 
 para make jobs
 
 # create the inversion bigBed and bigWig
-cat inversions/* |sort -k1,1 -k2,2n -k3,3n -k5,5n | chainArrangeCollect arrHumInv stdin stdout | awk '{print $0,$5}' >  $inversion.bed
-bedToBigBed  $inversion.bed /cluster/data/hg38/chrom.sizes $inversion.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+3
+cat inversions/* |sort -k1,1 -k2,2n -k3,3n -k5,5n | chainArrangeCollect arrHumInv stdin stdout | tawk '{print $0,$5, "# genomes in HPRC with inversion: "$5}' >  $inversion.bed
+bedToBigBed -tab  $inversion.bed /cluster/data/hg38/chrom.sizes $inversion.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+4
 cat inversions/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $inversion.bedGraph
 bedGraphToBigWig $inversion.bedGraph /cluster/data/hg38/chrom.sizes $inversion.bw
 mkdir -p /gbdb/hg38/hprcArr$VERSION
 rm -f  /gbdb/hg38/hprcArr$VERSION/$inversion.*
 ln -s `pwd`/$inversion.bw /gbdb/hg38/hprcArr$VERSION
 ln -s `pwd`/$inversion.bb /gbdb/hg38/hprcArr$VERSION
 
 # create the duplications bigBed and bigWig
-cat duplications/* |sort -k1,1 -k2,2n -k3,3n -k5,5n | chainArrangeCollect arrHumDup stdin stdout | awk '{print $0,$5}' > $duplication.bed
-bedToBigBed  $duplication.bed /cluster/data/hg38/chrom.sizes $duplication.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+3
+cat duplications/* |sort -k1,1 -k2,2n -k3,3n -k5,5n | chainArrangeCollect arrHumDup stdin stdout | tawk '{print $0,$5,  "# genomes in HPRC with duplication: "$5}' > $duplication.bed
+bedToBigBed -tab  $duplication.bed /cluster/data/hg38/chrom.sizes $duplication.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+4
 cat duplications/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $duplication.bedGraph
 bedGraphToBigWig $duplication.bedGraph /cluster/data/hg38/chrom.sizes $duplication.bw
 mkdir -p /gbdb/hg38/hprcArr$VERSION
 rm -f  /gbdb/hg38/hprcArr$VERSION/$duplication.*
 ln -s `pwd`/$duplication.bw /gbdb/hg38/hprcArr$VERSION
 ln -s `pwd`/$duplication.bb /gbdb/hg38/hprcArr$VERSION
 
 #below not done anymore
 
 # create the sum of duplications and inversions bigBed and bigWig
 cat inversions/* duplications/* |sort -k1,1 -k2,2n | chainArrangeCollect stdin stdout | awk '{print $0,$5}' > $all.bed
 bedToBigBed  $all.bed /cluster/data/hg38/chrom.sizes $all.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+1
 cat inversions/* duplications/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $all.bedGraph
 bedGraphToBigWig $all.bedGraph /cluster/data/hg38/chrom.sizes $all.bw
 mkdir -p /gbdb/hg38/hprcArr$VERSION
 rm -f  /gbdb/hg38/hprcArr$VERSION/$all.*
 ln -s `pwd`/$all.bw /gbdb/hg38/hprcArr$VERSION
 ln -s `pwd`/$all.bb /gbdb/hg38/hprcArr$VERSION