====== run-mummer4.sh ======

  #!/bin/sh
  #
  # run-mummer4.sh: MUMmer-based shell script for aligning draft sequences to a 
  #                 finished genome. 
  #
  
  if [ $# = 0 ]
      then 
          echo "Usage : run-mummer4.sh <prefix> <ref_seq_file> <query_seq_file> [-q]" 1>&2
          echo "The last option is for delta-filter."
          echo "Other nucmer default options: -maxmatch -c 100"
            exit 1
  fi
  
  #nucmer --prefix=$1 -mum -c 100 $2 $3
  nucmer --prefix=$1 -mum -c 1000 $2 $3
  
  if [ "$4" = "-q" ] 
      then
          delta-filter $4 $1.delta > tmp
          mv $1.delta $1.delta.org
          mv tmp $1.delta
  fi
  
  show-coords -rcl $1.delta > $1.coords
  
  REFNAME=`awk '$1~/^>/{print $1}' $2 | sed 's/^>//'`
  
  for QRYNAME in `awk '$1~/^>/{print $1}' $3 | sed 's/^>//'`
  do
      show-aligns $1.delta $REFNAME $QRYNAME > $1.aligns
  done
  
  mummerplot --postscript $1.delta -R $2 -Q $3  --layout --prefix=$1