7fda78a4052001b31148cdc2167dfc6dae8b0eee
braney
  Tue Feb 13 10:54:38 2024 -0800
starting again on quickLift

diff --git src/hg/makeDb/doc/hg38/hprcQuickLift.txt src/hg/makeDb/doc/hg38/hprcQuickLift.txt
new file mode 100644
index 0000000..40cf901
--- /dev/null
+++ src/hg/makeDb/doc/hg38/hprcQuickLift.txt
@@ -0,0 +1,35 @@
+mkdir -p /hive/data/genomes/hg38/bed/hprc/quickLift
+cd /hive/data/genomes/hg38/bed/hprc/quickLift
+
+mkdir chain
+for i in ../chain/*.chain
+do 
+f=`basename $i .chain`
+echo chainSwap $i chain/$f.swap.chain
+done > jobs
+
+sh -x jobs
+
+mkdir sizes
+for i in chain/*.chain
+do
+f=`basename $i .swap.chain`
+o=`echo $f | sed 's/hg38.chainHprc//'`
+echo $o
+awk '/chain/ {print $3, $4}' $i | sort | uniq > sizes/$o
+done
+
+mkdir bigChain
+for i in chain/*.chain
+do
+f=`basename $i .swap.chain`
+o=`echo $f | sed 's/hg38.chainHprc//'`
+rm -f tmp.bigChain tmp.bigChain.bigLink
+hgLoadChain -noBin -test hg38 bigChain $i
+sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > tmp.bigChain
+bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab tmp.bigChain sizes/$o bigChain/$o.bb
+awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n > tmp.bigChain.bigLink
+bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab tmp.bigChain.bigLink sizes/$o  bigChain/$o.link.bb
+done
+
+