To print 0 instead of undef, you can use the defined-or // operator. It needs Perl 5.10, otherwise you have to be more verbose (defined $_ ? $_ : 0).

#!/usr/bin/env perl
use warnings;
use strict;
use feature qw{ say };

use List::Util qw{ first };

my $IN = *DATA{IO};
my %hits;

my @headers = split ' ', <$IN>;
my $index = first { $headers[$_] eq 'Strand' } 0 .. $#headers;
while (<$IN>) {
    chomp;
    my @F = split ' ';
    $hits{ $F[ $index + 1 ] }{ $F[ $index + 2 ] }{ $F[$index] }++;
}

for my $key (keys %hits) {
    for my $inner_key (keys %{ $hits{$key} }) {
        say join "\t", $key, $inner_key,
            map $_ // 0, @{ $hits{$key}{$inner_key} }{qw{ c w }};
    }
}

__DATA__
Strand
c    8    336158    75    75M    74
c    12    828707    74    74M    73
w    10    528559    74    74M    0
c    15    267766    74    74M    73
c    12    828707    74    74M    73
c    14    491797    74    74M    73
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Have you noticed I used $_ only in map and first? Both chomp and split work with it by default. If you feel the need to explicitly type the argument, name the variable.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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