use strict;
use warnings;

my $data = <<DATA;
CLS_S3_Contig100_st,CLS_S3_Contig100,13,10,0.3717
CLS_S3_Contig100_st,CLS_S3_Contig100,53,10,0.3717
CLS_S3_Contig10031_st,CLS_S3_Contig10031,53,12,0.5548
CLS_S3_Contig10031_st,CLS_S3_Contig10031,57,10,0.4871
CLS_S3_Contig10031_st,CLS_S3_Contig10031,61,12,0.547
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,62,11,0.5129
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,64,11,0.5789
DATA

my %origins;
my $numColumns;

open my $inFile, '<', \$data;
while (<$inFile>) {
    chomp;
    next unless length;
    
    my @columns = split ',';
    
    $numColumns ||= @columns; # Assume first row has correct column count
    $origins{$columns[1]}[$columns[2] - 1] = \@columns;
}
close $inFile;


for my $oKey (sort keys %origins) {
    my $origin = $origins{$oKey};
    my $lastAdded = -1;

    # Fake up present flag for +/- 8 lines around real data
    for my $pip (0 .. $#$origin) {
        next if $pip <= $lastAdded or ! defined $origin->[$pip];

        my $first = $pip > 8 ? $pip - 8 : 0;
        my $last = $pip + 8;
        
        $last = $#$origin if $last > $#$origin;
        for my $index ($first .. $last) {
            next if defined $origin->[$index];
            
            @{$origin->[$index]}[0 .. $numColumns - 1] =
                ('', $oKey, $index + 1, ('') x $numColumns);
        }
        
        $lastAdded = $last;
    }

    # Now output the result
    for my $pip (0 .. $#$origin) {
        my $row = $origin->[$pip];
        
        if (defined $row) {
            # pip exists in original file
            print join (",", @$row, '1'), "\n";
        } else {
            # pip doesn't exist in original file
            print ",$oKey,", $pip + 1, ',' x ($numColumns - 2), "0\n";
        }
    }
}

##</code><code>##

...
,CLS_S3_Contig100,4,,,0
,CLS_S3_Contig100,5,,,1
,CLS_S3_Contig100,6,,,1
,CLS_S3_Contig100,7,,,1
,CLS_S3_Contig100,8,,,1
,CLS_S3_Contig100,9,,,1
,CLS_S3_Contig100,10,,,1
,CLS_S3_Contig100,11,,,1
,CLS_S3_Contig100,12,,,1
CLS_S3_Contig100_st,CLS_S3_Contig100,13,10,0.3717,1
,CLS_S3_Contig100,14,,,1
,CLS_S3_Contig100,15,,,1
,CLS_S3_Contig100,16,,,1
,CLS_S3_Contig100,17,,,1
,CLS_S3_Contig100,18,,,1
,CLS_S3_Contig100,19,,,1
,CLS_S3_Contig100,20,,,1
,CLS_S3_Contig100,21,,,1
,CLS_S3_Contig100,22,,,0
,CLS_S3_Contig100,23,,,0
...
,CLS_S3_Contig100,43,,,0
,CLS_S3_Contig100,44,,,0
,CLS_S3_Contig100,45,,,1
,CLS_S3_Contig100,46,,,1
,CLS_S3_Contig100,47,,,1
,CLS_S3_Contig100,48,,,1
,CLS_S3_Contig100,49,,,1
,CLS_S3_Contig100,50,,,1
,CLS_S3_Contig100,51,,,1
,CLS_S3_Contig100,52,,,1
CLS_S3_Contig100_st,CLS_S3_Contig100,53,10,0.3717,1
,CLS_S3_Contig10031,1,,,0
...
,CLS_S3_Contig10031,44,,,0
,CLS_S3_Contig10031,45,,,1
,CLS_S3_Contig10031,46,,,1
,CLS_S3_Contig10031,47,,,1
,CLS_S3_Contig10031,48,,,1
,CLS_S3_Contig10031,49,,,1
,CLS_S3_Contig10031,50,,,1
,CLS_S3_Contig10031,51,,,1
,CLS_S3_Contig10031,52,,,1
CLS_S3_Contig10031_st,CLS_S3_Contig10031,53,12,0.5548,1
,CLS_S3_Contig10031,54,,,1
,CLS_S3_Contig10031,55,,,1
,CLS_S3_Contig10031,56,,,1
CLS_S3_Contig10031_st,CLS_S3_Contig10031,57,10,0.4871,1
,CLS_S3_Contig10031,58,,,1
,CLS_S3_Contig10031,59,,,1
,CLS_S3_Contig10031,60,,,1
CLS_S3_Contig10031_st,CLS_S3_Contig10031,61,12,0.547,1
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,62,11,0.5129,1
,CLS_S3_Contig10031,63,,,1
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,64,11,0.5789,1