#!/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 (csts-export)"
    echo "          to_dir - ../merge-import"
    echo "from_dir files: *-??"
    echo "to_dir files: *-??-??"
    exit 1
}

fdir="."
tdir="../merge-import"
ddir="../merge-import-done"
zdir="../merge-zero"

while getopts f:h FLAG; do
    case $FLAG in
	f) fdir=$OPTARG ;;
	h) print_help ;;
#	t) tdir=$OPTARG; ddir=$tdir-done; zdir=${tdir%-import}-zero ;;
        *) echo "Unknown option \"$1\""; print_help ;;
    esac
done

cd $fdir

mkdir -p $tdir;
mkdir -p $ddir;
mkdir -p $zdir;

ff=''
aa=''
cd $fdir
for gg in *-??; do
    bb=${gg%-??}
    if [ "x$aa" = "x$bb" ]; then
	if [[ ! -f $tdir/$ff${gg: -3}  ]] && [[ ! -f $ddir/$ff${gg: -3} ]] && [[ ! -f $zdir/$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