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/hprcInDel.txt src/hg/makeDb/doc/hg38/hprcInDel.txt
index f57fad4..5452755 100644
--- src/hg/makeDb/doc/hg38/hprcInDel.txt
+++ src/hg/makeDb/doc/hg38/hprcInDel.txt
@@ -8,29 +8,29 @@
 rm -rf topLevel
 mkdir topLevel
 for i in ../chain/*.chain; do f=`basename $i .chain`;echo netChainSubset ../net/$f.net $i topLevel/$f.chain -type=top; done > subset.jobs
 para make subset.jobs
 
 rm -rf indels
 mkdir indels
 for chain in topLevel/*.chain; do 
 name=`basename $chain | sed 's?.*chainHprc??' | sed 's/\.chain//'`
 echo chainInDel $chain $name indels/$name.txt
 done > indel.jobs
 para make indel.jobs
 
 sort -S 50G -k1,1 -k2,2n -k3,3n -k5,5n indels/* > sortIndels.bed
 
-awk '{if (($3 > $2) && ($5 == 0)) print}' sortIndels.bed | chainArrangeCollect -exact arrHumDel stdin stdout | awk '{$11=$3-$2;print $0,$5"-"$3 - $2"bp" }' > $deletions.bed
-bedToBigBed  $deletions.bed /cluster/data/hg38/chrom.sizes $deletions.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+3
+tawk '{if (($3 > $2) && ($5 == 0)) print}' sortIndels.bed | chainArrangeCollect -exact arrHumDel stdin stdout | tawk '{$11=$3-$2;print $0,$5":"$3 - $2"bp", "# genomes in HPRC with ins: "$5"<BR>Size of ins: "$3 - $2"bp"}' > $deletions.bed
+bedToBigBed -tab  $deletions.bed /cluster/data/hg38/chrom.sizes $deletions.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+4
 rm -f  /gbdb/hg38/hprcArr$VERSION/$deletions.bb
 ln -s `pwd`/$deletions.bb /gbdb/hg38/hprcArr$VERSION
 
-awk '{if ($3 == $2) print}' sortIndels.bed | chainArrangeCollect -exact arrHumIns stdin stdout | awk '{print $0,$5"-"$11"bp" }' >$inserts.bed
-bedToBigBed  $inserts.bed /cluster/data/hg38/chrom.sizes $inserts.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+3
+tawk '{if ($3 == $2) print}' sortIndels.bed | chainArrangeCollect -exact arrHumIns stdin stdout | tawk '{print $0,$5":"$11"bp","# genomes in HPRC with del: "$5"<BR>Size of del: "$11"bp" }' >$inserts.bed
+bedToBigBed -tab  $inserts.bed /cluster/data/hg38/chrom.sizes $inserts.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+4
 rm  -f /gbdb/hg38/hprcArr$VERSION/$inserts.bb
 ln -s `pwd`/$inserts.bb /gbdb/hg38/hprcArr$VERSION
 
-awk '{if (($3 > $2) && ($5 != 0)) print}' sortIndels.bed | chainArrangeCollect -exact arrHumOth stdin stdout | awk '{print $0,$5"-"$11"bp-"$3-$2"bp" }' >$double.bed
-bedToBigBed  $double.bed /cluster/data/hg38/chrom.sizes $double.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+3
+tawk '{if (($3 > $2) && ($5 != 0)) print}' sortIndels.bed | chainArrangeCollect -exact arrHumOth stdin stdout | tawk '{print $0,$5":"$11"bp-"$3-$2"bp","# genomes in HPRC with ins: "$5"<BR>Size of ins: "$3-$2"bp<BR>Size of del: "$11"bp"  }' >$double.bed
+bedToBigBed -tab  $double.bed /cluster/data/hg38/chrom.sizes $double.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+4
 rm  -f /gbdb/hg38/hprcArr$VERSION/$double.bb
 ln -s `pwd`/$double.bb /gbdb/hg38/hprcArr$VERSION