#!/bin/bash
#
# KO_Female.12WK.mm39.scaled.combinedJunctions.bed

for bed in $(ls *.bed); do
   bed2=${bed/.bed/.bed2};
   if [ ! -f ${bed2} ]; then
      echo "Copying to ${bed2}";
      mv ${bed} ${bed2};
   fi;
done;

for bed2 in $(ls *.bed2); do
   bed=${bed2/.bed2/.bed};
   if [ ! -f ${bed} ]; then
      echo "Repairing to ${bed}";
      cat ${bed2} | perl -p -e 's/\t([-+*])\t([0-9][.][0-9]+)\t/\t$2\t$1\t/;' > ${bed}
   fi;
done;