Thank your very much GrandFather,

The code works perfect, but when the gap between two adjacent PIP in the original file is large let's say 16 or more it behaves differently.

Please take a look at the input and output files I have included here. In the output after 949 it has printed three "1"s instead of 8.

I went through the code and I think a condition should be added here. To see if the gap in pip is greater or equal to 16. is my speculation right? 

my $first = $pip > 8 ? $pip - 8 : 0;
        my $last = $pip + 8;

[download]
Original 

CLS_S3_Contig1000       933     10      0.488
CLS_S3_Contig1000       935     9       0.4867
CLS_S3_Contig1000       937     9       0.4989
CLS_S3_Contig1000       939     10      0.503
CLS_S3_Contig1000       943     8       0.3531
CLS_S3_Contig1000       949     8       0.3477
CLS_S3_Contig1000       1060    6       0.1498
CLS_S3_Contig1000       1070    9       0.3885
CLS_S3_Contig1000       1071    8       0.3848


OUTPUT

CLS_S3_Contig1000       933     10      0.488   1
CLS_S3_Contig1000       934                     1
CLS_S3_Contig1000       935     9       0.4867  1
CLS_S3_Contig1000       936                     1
CLS_S3_Contig1000       937     9       0.4989  1
CLS_S3_Contig1000       938                     1
CLS_S3_Contig1000       939     10      0.503   1
CLS_S3_Contig1000       940                     1
CLS_S3_Contig1000       941                     1
CLS_S3_Contig1000       942                     1
CLS_S3_Contig1000       943     8       0.3531  1
CLS_S3_Contig1000       944                     1
CLS_S3_Contig1000       945                     1
CLS_S3_Contig1000       946                     1
CLS_S3_Contig1000       947                     1
CLS_S3_Contig1000       948                     1
CLS_S3_Contig1000       949     8       0.3477  1
CLS_S3_Contig1000       950                     1
CLS_S3_Contig1000       951                     1
CLS_S3_Contig1000       952                     0
CLS_S3_Contig1000       953                     0
CLS_S3_Contig1000       954                     0
CLS_S3_Contig1000       955                     0
CLS_S3_Contig1000       956                     0
CLS_S3_Contig1000       957                     0

[download]

In reply to Re^2: Hash_of_Hash_Would do it? by Anonymous Monk
in thread Hash_of_Hash_Would do it? by sesemin

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