Convert exon-intron list to junction list

exonIntronList2JunctionList.awk

BEGIN {
    FS="\t";
    old_chr = "chrN";
    old_start = -1;
    old_stop = -1;
    old_id = "*";
    old_score = "*";
    old_strand = "*";
}
{
    new_chr = $1;
    new_start = $2;
    new_stop = $3;
    new_id = $4;
    new_score = $5;
    new_strand = $6;

    if (old_id != new_id) {
        # new element                                                                                                                                                                                                                                                             
        old_id = new_id;
    }
    else {
        # construct and print junction                                                                                                                                                                                                                                            
        old_score = 2;
        print old_chr"\t"old_stop"\t"(old_stop+1)"\t"old_id"\t"old_score"\t"old_strand;
    }

    old_chr = new_chr;
    old_start = new_start;
    old_stop = new_stop;
    old_id = new_id;
    old_score = new_score;
    old_strand = new_strand;
}
END {
}