7d86e0ffbe4295c91220ff671c3eeb2009d41408
braney
  Sun Feb 25 11:09:39 2024 -0800
working on quickLift UI

diff --git src/hg/makeDb/doc/hg38/hprcQuickLift.txt src/hg/makeDb/doc/hg38/hprcQuickLift.txt
index 40cf901..cbadd3b 100644
--- src/hg/makeDb/doc/hg38/hprcQuickLift.txt
+++ src/hg/makeDb/doc/hg38/hprcQuickLift.txt
@@ -1,35 +1,46 @@
 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
 
+mkdir -p /gbdb/hg38/quickLift
+rm tableData.txt
+for i in bigChain/*.link.bb
+do
+s=`basename $i .link.bb`.bb
+db=`basename $s .bb`
+f=/gbdb/hg38/quickLift/$s
+echo ln -s `pwd`/bigChain/$s $f
+echo "0 hg38 $db $f" | tr ' ' '\t' >> tableData.txt
+done
 
+hgLoadSqlTab hgcentraltest quickLiftChain $HOME/kent/src/hg/lib/quickLiftChain.sql tableData.txt