#!/bin/bash

print_help() {
    echo "Merge two annotations and prepare data for final annotation"
    echo "Usage: $(basename "$0") [ -f from_dir ] [ -t to_dir ]"
    echo "       $(basename "$0") -h"
    echo "Defaults: from_dir - current dir"
    echo "          to_dir - ../merge-import (must exist)"
    echo "from_dir files: *-??"
    echo "to_dir files: *-??-??"
    exit 1
}

fdir="."
tdir="../merge-import"

while getopts f:ht: FLAG; do
    case $FLAG in
	f) fdir=$OPTARG ;;
	h) print_help ;;
	t) tdir=$OPTARG ;;
        *) echo "Unknown option \"$1\""; print_help ;;
    esac
done

ff=''
aa=''
cd $fdir
for gg in *-??; do
    bb=${gg%-??}
    if [ "x$aa" = "x$bb" ]; then
	if [ ! -f $tdir/$ff${gg: -3} ]; then
	    echo "$ff${gg: -3}"
	    paste $ff $gg | perl -pe 's/"utkl-.."/"utkl"/g' \
		| merge-csts | remove-MM.pl > $tdir/$ff${gg: -3}
	fi
    fi
    aa=$bb
    ff=$gg
done