Well played. You've actually managed to post something that nobody has responded to yet - a good combination of proper documentation and high level of difficulty (or work at least). Here's one potential solution - you may notice that I've added a few records on the end so you can see how mean and median come out. What you do with the end data is of course up to you.

use Data::Dumper;
use strict;
use warnings;

my (%data, $k, $r, $n);

<DATA>;
while (<DATA>) {
    chomp; my %d;
    @d{qw/chr1 start end pos1 pos2 cgtype cov methy strand/} = split /
+\s+/;
    push @{$data{"$d{'chr1'}:$d{'start'}-$d{'end'}"}}, \%d;
}

for $k (sort {
    $data{$a}[0]{'chr1'} cmp $data{$b}[0]{'chr1'} ||
    $data{$a}[0]{'start'} <=> $data{$b}[0]{'start'} ||
    $data{$a}[0]{'end'} <=> $data{$b}[0]{'end'}
} keys %data) {
    my %d;
    $d{'cpg'} = $k;
    $d{'length'} = $#{$data{$k}} + 1;

    for $r (@{$data{$k}}) {
        if ($r->{'cgtype'} eq 'CG') {
            $d{'cg'}++;
            for $n (0, 5, 10) {
                if ($r->{'cov'} > $n) {
                    $d{"cg>$n"}++;
                    push @{$d{"cg>${n}vals"}}, $r->{'methy'};
                }
            }
        }
    }
    for $n (0, 5, 10) {
        if ($d{"cg>${n}vals"}) {
            $d{"cg>${n}mean"} += $_ for @{$d{"cg>${n}vals"}};
            $d{"cg>${n}mean"} /= $d{"cg>${n}"};
            @{$d{"cg>${n}vals"}} = sort { $a <=> $b } @{$d{"cg>${n}val
+s"}};
            if ($d{"cg>$n"} % 2 == 1) {
                $d{"cg>${n}median"} = $d{"cg>${n}vals"}[$d{"cg>$n"} / 
+2];
            }
            else {
                $d{"cg>${n}median"} = ($d{"cg>${n}vals"}[$d{"cg>$n"} /
+ 2 - 1] + $d{"cg>${n}vals"}[$d{"cg>$n"} / 2]) / 2;
            }
        }
        else {
            $d{"cg>${n}mean"} = 0;
            $d{"cg>${n}median"} = 0;
        }
    }

    ### DO SOMETHING WITH DATA
    use Data::Dumper;
    print Dumper(\%d);
}

__DATA__
chr    start    end    pos1    pos2    CGtype    Cov.    Methy    Stra
+nd    
chr1    18598    19673    18676    18676    CHH    0    0    +
chr1    18598    19673    18689    18689    CG    2    0    +
chr1    18598    19673    18997    18997    CHH    0    0    +
chr1    18598    19673    19546    19546    CG    4    0    +
chr1    18598    19673    19671    19671    CHG    7    0    +
chr1    124987    125426    125001    125001    CHH    1    0    +
chr1    124987    125426    125226    125226    CG    0    0    +
chr1    124987    125426    125426    125426    CG    0    0    +
chr1    317653    318092    317653    317653    CHG    11    0    +
chr1    317653    318092    317795    317795    CHG    0    0    +
chr1    317653    318092    318090    318090    CHH    3    0    +
chr1    427014    428027    427025    427025    CHH    0    0    +
chr1    439136    440407    439687    439687    CHH    9    0    +
chr1    523082    523977    523167    523167    CG    0    0    +
chr1    534601    536512    535789    535789    CHH    1    0    +
chr1    703847    704410    703999    703999    CHH    0    0    +
chr1    752279    753308    753330    753330    CHH    0    0    +
chr2    5000    100000    100000    100000    CG    1    9    +
chr2    5000    100000    100000    100000    CG    3    2    +
chr2    5000    100000    100000    100000    CG    6    7    +
chr2    5000    100000    100000    100000    CG    9    11    +
[download]