#!/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