合并坐标，考虑二元素

Question

如下表所示，将重复序列进行合并，如果两种重复序列在坐标上是有重合，则将两个重复序列合并成一个，输出。
请写清楚完整代码
我参考网上的写了一个但是发现无法统计染色体结果

use strict;
use warnings;
my @name_array ;
my $hash;
open (FILE, "trf.gff");
while(<FILE>){
        my ($scaff, $a, $b, $min, $max, $c, $d, $e, $f, $g, $class, $h, $i, $j) = split(/\t|;/);   #是对的
        unless (grep $_->[8] eq $class ,@name_array){
                push  @name_array, [$scaff, $a, $b, $c, $d, $e, $f, $g, $class, $h, $i, $j];
        } ;

        ($min,$max) = ($max,$min) if $min > $max ;

        if($hash->{$class}){
                sort_matrix($min,$max,$hash->{$class});
        }
        else{
                push @{$hash->{$class}},[$min,$max];
        }

}
###print sort result
for my $item( @name_array ){
        my $class = $item->[8];
        for (0..$#{$hash->{$class}}){
                print $item->[0]," ",$item->[1]," ",$item->[2]," ",$hash->{$class}->[$_][0]," ",$hash->{$class}->[$_][1]," ",$item->[3]," ",$item->[4]," ",$item->[5]," ",$item->[6]," ",$item->[7]," ",$class,"_E",($_+1)," ",$item->[9]," ",$item->[10]," ",$item->[11],"\n";
        }
}

sub sort_matrix{
        my ($cur_min,$cur_max,$matrix) = @_;
        # record index
        my @splice_index;
        for (0..$#$matrix){
                my $item_min = $matrix->[$_]->[0];
                my $item_max = $matrix->[$_]->[1];
                next if $cur_max < $item_min or $cur_min > $item_max;
                return if $cur_min >= $item_min and $cur_max <= $item_max;
                $cur_min  = $cur_min < $item_min ? $cur_min : $item_min;
                $cur_max = $cur_max < $item_max ? $item_max : $cur_max;
                push @splice_index, $_;
        }
        push @$matrix,[$cur_min,$cur_max];
        #print "@splice_index\n";

        for (0..$#splice_index){
                splice(@$matrix,$splice_index[$_]-$_,1);##This is trick
        }
        #print $cur_min,":",$cur_max,"\n";
}

Answer 1

坐标是啥，染色体又是啥？两种重复序列是什么意思？另外，只考虑perl吗？其他语言实现ok不？