I thought I would provide another approach that doesn't use a hash. It processes line by line.

Chris 

#!/usr/bin/perl
use strict;
use warnings;

chomp(my @previous = split /\t/, <DATA>);

my $from = 1;
my $to = $previous[2]-9 > 0 ? $previous[2]-9 : 0;

# print '0 values' up to 8 less of margin
for my $pos ($from..$to) {
    print join("\t", $previous[1], $pos, '','','0'), "\n";
}

$from = $previous[2]-8 > 0 ? $previous[2]-8 : 1;
$to = $previous[2]-1;

# print margin of '1 values' up to first record
for my $pos ($from .. $to) {
    print join("\t", $previous[1], $pos, '','','1'), "\n";
}

# print first record
print join("\t", @previous[1..4], '1'), "\n";
my $pos_count = $previous[2];

while (<DATA>) {
    chomp;
    my @current= split /\t/;
    
    if ($current[1] eq $previous[1]) {
        if (++$pos_count != $current[2]) {
            for my $pos ($pos_count .. $current[2]-1) {
                print join("\t", $current[1], $pos, '','', '1'), "\n";
            }
        }
        print join("\t", @current[1..4], 1), "\n";
    }
    else {
        # print '1 values' for margin of 8 past last pos for previous 
+record
        for my $pos ($previous[2] + 1 .. $previous[2] + 8) {
            print join("\t", $previous[1], $pos, '','','1'), "\n";
        }
        
        $from = 1;
        $to = $current[2]-9 > 0 ? $current[2]-9 : 0;
        
        # print '0 values' up to 8 less of margin for current record
        for my $pos ($from .. $to) {
            print join("\t", $current[1], $pos, '','','0'), "\n";
        }
        
        $from = $current[2]-8 > 0 ? $current[2]-8 : 1;
        $to = $current[2]-1;
        
        # print '1 values' up to current record
        for my $pos ($from .. $to) {
            print join("\t", $current[1], $pos, '','','1'), "\n";
        }
        
        print join("\t", @current[1..4], 1), "\n";
    }
    
    $pos_count = $current[2];
    @previous = @current;
}

# after last record printed, print out margin of 8 more
for my $pos ($previous[2] + 1 .. $previous[2] + 8) {
    print join("\t", $previous[1], $pos, '','','1'), "\n";
}


__DATA__
CLS_S3_Contig100_st    CLS_S3_Contig100    53    10    0.3717
CLS_S3_Contig100_at    CLS_S3_Contig100    55    11    0.4321
CLS_S3_Contig100_st    CLS_S3_Contig100    57    10    0.3223
CLS_S3_Contig100_at    CLS_S3_Contig100    59    11    0.4055
CLS_S3_Contig100_st    CLS_S3_Contig100    61    11    0.4511
CLS_S3_Contig100_at    CLS_S3_Contig100    63    11    0.474
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

[download]
It printed out this solution. 

CLS_S3_Contig100    1            0
CLS_S3_Contig100    2            0
CLS_S3_Contig100    3            0
CLS_S3_Contig100    4            0
CLS_S3_Contig100    5            0
CLS_S3_Contig100    6            0
CLS_S3_Contig100    7            0
CLS_S3_Contig100    8            0
CLS_S3_Contig100    9            0
CLS_S3_Contig100    10            0
CLS_S3_Contig100    11            0
CLS_S3_Contig100    12            0
CLS_S3_Contig100    13            0
CLS_S3_Contig100    14            0
CLS_S3_Contig100    15            0
CLS_S3_Contig100    16            0
CLS_S3_Contig100    17            0
CLS_S3_Contig100    18            0
CLS_S3_Contig100    19            0
CLS_S3_Contig100    20            0
CLS_S3_Contig100    21            0
CLS_S3_Contig100    22            0
CLS_S3_Contig100    23            0
CLS_S3_Contig100    24            0
CLS_S3_Contig100    25            0
CLS_S3_Contig100    26            0
CLS_S3_Contig100    27            0
CLS_S3_Contig100    28            0
CLS_S3_Contig100    29            0
CLS_S3_Contig100    30            0
CLS_S3_Contig100    31            0
CLS_S3_Contig100    32            0
CLS_S3_Contig100    33            0
CLS_S3_Contig100    34            0
CLS_S3_Contig100    35            0
CLS_S3_Contig100    36            0
CLS_S3_Contig100    37            0
CLS_S3_Contig100    38            0
CLS_S3_Contig100    39            0
CLS_S3_Contig100    40            0
CLS_S3_Contig100    41            0
CLS_S3_Contig100    42            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    53    10    0.3717    1
CLS_S3_Contig100    54            1
CLS_S3_Contig100    55    11    0.4321    1
CLS_S3_Contig100    56            1
CLS_S3_Contig100    57    10    0.3223    1
CLS_S3_Contig100    58            1
CLS_S3_Contig100    59    11    0.4055    1
CLS_S3_Contig100    60            1
CLS_S3_Contig100    61    11    0.4511    1
CLS_S3_Contig100    62            1
CLS_S3_Contig100    63    11    0.474    1
CLS_S3_Contig100    64            1
CLS_S3_Contig100    65            1
CLS_S3_Contig100    66            1
CLS_S3_Contig100    67            1
CLS_S3_Contig100    68            1
CLS_S3_Contig100    69            1
CLS_S3_Contig100    70            1
CLS_S3_Contig100    71            1
CLS_S3_Contig10031    1            0
CLS_S3_Contig10031    2            0
CLS_S3_Contig10031    3            0
CLS_S3_Contig10031    4            0
CLS_S3_Contig10031    5            0
CLS_S3_Contig10031    6            0
CLS_S3_Contig10031    7            0
CLS_S3_Contig10031    8            0
CLS_S3_Contig10031    9            0
CLS_S3_Contig10031    10            0
CLS_S3_Contig10031    11            0
CLS_S3_Contig10031    12            0
CLS_S3_Contig10031    13            0
CLS_S3_Contig10031    14            0
CLS_S3_Contig10031    15            0
CLS_S3_Contig10031    16            0
CLS_S3_Contig10031    17            0
CLS_S3_Contig10031    18            0
CLS_S3_Contig10031    19            0
CLS_S3_Contig10031    20            0
CLS_S3_Contig10031    21            0
CLS_S3_Contig10031    22            0
CLS_S3_Contig10031    23            0
CLS_S3_Contig10031    24            0
CLS_S3_Contig10031    25            0
CLS_S3_Contig10031    26            0
CLS_S3_Contig10031    27            0
CLS_S3_Contig10031    28            0
CLS_S3_Contig10031    29            0
CLS_S3_Contig10031    30            0
CLS_S3_Contig10031    31            0
CLS_S3_Contig10031    32            0
CLS_S3_Contig10031    33            0
CLS_S3_Contig10031    34            0
CLS_S3_Contig10031    35            0
CLS_S3_Contig10031    36            0
CLS_S3_Contig10031    37            0
CLS_S3_Contig10031    38            0
CLS_S3_Contig10031    39            0
CLS_S3_Contig10031    40            0
CLS_S3_Contig10031    41            0
CLS_S3_Contig10031    42            0
CLS_S3_Contig10031    43            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    53    12    0.5548    1
CLS_S3_Contig10031    54            1
CLS_S3_Contig10031    55            1
CLS_S3_Contig10031    56            1
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    61    12    0.547    1
CLS_S3_Contig10031    62    11    0.5129    1
CLS_S3_Contig10031    63            1
CLS_S3_Contig10031    64    11    0.5789    1
CLS_S3_Contig10031    65            1
CLS_S3_Contig10031    66            1
CLS_S3_Contig10031    67            1
CLS_S3_Contig10031    68            1
CLS_S3_Contig10031    69            1
CLS_S3_Contig10031    70            1
CLS_S3_Contig10031    71            1
CLS_S3_Contig10031    72            1

[download]

In reply to Re: Hash_of_Hash_Would do it? by Cristoforo
in thread Hash_of_Hash_Would do it? by sesemin

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