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Line_1:Line_1_1
Line_2:Line_2_2
Line_3:Line_3_3
Line_4:Line_4_4

Line_5:Line_5_5
Line_6:Line_6_6

Line_7:Line_7_7
Line_8:Line_8_8
Line_9:Line_9_9
Line_10:Line_10_10

my $i = 0;
while (<>) { # read from @ARGV
...
    push @{ $value[$i++] }, /:([^:]+)/; # get timestamp
    $i = 0 if eof;
}

my $i = 0;
my $filecount = 0;
...
        ++$filecount;
    }
}

if (!exists $value[$line]->[$file]) {
  # no value assigned, there is a hole in the array
} else {
  # value assigned
}