update_liftOverChain

#!/usr/bin/env bash

mkdir -p /gbdb/liftOver

if [ "$(ls -A /gbdb/liftOver)" ]; then

  for i in $(ls -1 /gbdb/liftOver/*.chain.gz); do
    j=$(basename $i)
    k=$(echo $j  | sed -nr 's/^(.*)_to_(.*)\.chain\.gz/\1\t\2/p')
    echo -e "$k\t$i\t0.95\t0\t0\tN\t1\tN"
  done > /tmp/liftOverChain.tsv

  hgsql -e "delete from hgcentral.liftOverChain"
  hgsql -e "load data local infile \"/tmp/liftOverChain.tsv\" into table hgcentral.liftOverChain;"
else
  echo "No liftover chain files found"
fi