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
