2e2674507b0968331df3f081e65b08678f860ca3
braney
  Sat Oct 14 16:45:14 2023 -0700
some cleanup of the HPRC tracks

diff --git src/hg/makeDb/doc/hg38/hprcRearrange.txt src/hg/makeDb/doc/hg38/hprcRearrange.txt
index 93ad8c0..d9ce4f8 100644
--- src/hg/makeDb/doc/hg38/hprcRearrange.txt
+++ src/hg/makeDb/doc/hg38/hprcRearrange.txt
@@ -1,39 +1,37 @@
 # 2023-08-12 braney
 
 VERSION=V1
 inversion=hprcArrInv$VERSION
 duplication=hprcArrDup$VERSION
 all=hprcArrAll$VERSION
 
 mkdir -p /cluster/data/hg38/bed/hprcArrange$VERSION
 cd /cluster/data/hg38/bed/hprcArrange$VERSION
 
 # grab the chains
-ls /hive/data/genomes/hg38/bed/hprc/bigChains/*.bb | grep -v Link > bigChain.lst
-ls /hive/data/genomes/hg38/bed/hprc/bigChains/*.bb | grep Link > bigLink.lst
-paste bigChain.lst bigLink.lst > both.lst
+ls /hive/data/genomes/hg38/bed/hprc/reChain/*.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 link 
+while read chain 
 do
-name=`basename $chain | sed 's?-.*??' | sed 's/.bb//'`
-echo bigChainArrange $chain $link $name inversions/$name.txt duplications/$name.txt
-done < both.lst > jobs
+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 | bedCollect stdin $inversion.bed
 bedToBigBed  $inversion.bed /cluster/data/hg38/chrom.sizes $inversion.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+1
 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 | bedCollect stdin $duplication.bed
@@ -43,15 +41,16 @@
 mkdir -p /gbdb/hg38/hprcArr$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
 
 # create the sum of duplications and inversions bigBed and bigWig
 cat inversions/* duplications/* |sort -k1,1 -k2,2n | bedCollect stdin $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
 
+