#!/bin/sh -e
#
# Find exact tandem repeats in specified file involving an
# exact duplicate of at least the specified length

usage () {
    echo "Usage: `basename $0` <file> <min-match-len>"
    return 67 # EX_USAGE
}

if [ $# -ne 2 ] ; then
    echo "You provided $# arguments instead of 2."
    usage
fi

filename="$1"
matchlen="$2"

bindir=/usr/bin
scriptdir=/usr/lib/mummer

if  [ ! -e "$filename"  ] ; then
    echo "File $filename does not exist."
    usage
fi

echo "Finding matches"
$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.tmp.matches
# This is default behavior when shell started with -e
# if  ($status != 0)  exit -1

echo "Tandem repeats"
sort -k1n -k2n $$.tmp.matches | awk -f $
$scriptdir/tandem-repeat.awk
rm -f $$.tmp.matches
