#!/bin/sh -e
#
# **SEVERELY** antiquated script for running the mummer 1 suite
# -r option reverse complements the query sequence, coordinates of the reverse
# matches will be relative to the reversed sequence
#

usage () {
    echo "Usage: `basename $0` <fasta reference> <fasta query> <prefix> [-r]"
    return 67 # EX_USAGE
}

if [ $# -ne 3 -a $# -ne 4 ] ; then
    echo "You provided $# arguments."
    usage
fi

ref="$1"
qry="$2"
pfx="$3"
rev="$4"

bindir=/usr/bin

if  [ ! -e "$ref"  ] ; then
    echo "File for fasta reference $ref does not exist."
    usage
fi

if  [ ! -e "$qry"  ] ; then
    echo "File for fasta query $qry does not exist."
    usage
fi

if [ "$pfx" = "" ] ; then
    usage
fi

echo "Find MUMs"
$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out
echo "Determine gaps"
$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps
echo "Align gaps"
$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align
mv witherrors.gaps "$pfx".errorsgaps
