You should be more specific in your definition of "sorted". Look at my solution elsewhere in this thread. If you mean that the 2nd, 3rd and 4th column being sorted numeric, that isn't very hard either: use pack/unpack

my @key   = qw( chr fivep threep strand );
my @files = qw( file1.tab file2.tab );

my %c7;
foreach my $file (@files) {
    csv (
    in      => $file,
    out     => undef,
    sep     => "\t",
    on_in   => sub { $c7{pack "A10l>l>l>", @{$_[1]}[0..3]}{$file} = $_
+[1][6] }
    );
    }

say join "\t" => @key, @files;
foreach my $key (sort keys %c7) {
    say join "\t" => (unpack "A10l>l>l>" => $key), map { $c7{$key}{$_}
+ // 0 } @files;
    }
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What is // doing in the above code?

// in this case is the Logical Defined Or (as opposed to the empty regular expression, for example in "$foo =~ //;"). The expression $data{$key}{$file} // 0 is the same as defined($data{$key}{$file}) ? $data{$key}{$file} : 0