计算vcf文件中SV的长度

#!/usr/bin/perl/ -w
use strict;

##useage:perl get.pl ref.vcf map out
###ref  chr1    4357    DUP00000001     G       <DUP>   1560    PASS    IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.6;END=16430;
##map     1     DEL00000015 0   27720

open IN,"<$ARGV[0]";

open MA,"<$ARGV[1]";

open OU,">$ARGV[2]";

my %MA=();
my $pos;
while(<MA>){
    chomp;
    my @ma=split/\t/;
    my $pos=$ma[3];
    $MA{$ma[1]}=$ma[3];


}


while (<IN>){
    chomp;
    my @ref=split;
    my $chr=$ref[0];
    my $str=$ref[1];
    my $id=$ref[2];
    my @end=$ref[7]=~/(\d+)/g; ###提取所有数字
    my $en=$end[3];##第四个匹配的就是end值
    my $len=$en-$str+1;
    if (exists $MA{$id}){   
    print OU "$id\t$chr\t$str\t$len\n";
}   
}

close MA;
close ref;
close OU;