Hi all, I've a file with 12 column with the following format: read_no,read_name,read_len,read_position_begin,read_position_end,reference_seq_no,reference_position_begin,reference_position_end,reversed,no_of_match,paired,alignment_score Example of the file: 
223445 BG2A093.x1    51    7     51    4    75    96    0 1    0    44
223446 BG2A073.x1    51    7     51    4    43    95    0 1    0    44
223447 BG2A033.x1    51    7     51    4    44    92    0 1    0    42
223448 BG2A693.x1    51    7     51    4    45    93    1 1    0    43
223449 BG2A045.x1    51    7     51    4    47    95    1 1    0    47
223501 BG2A034.x1    51    7     51    4    47    95    0 1    0    46
223442 BG2A021.x1    51    7     51    4    48    96    0 1    0    45

[download]
What I'm trying to do is to add a number next to column no.7, so that whenever there is an duplication in column 7 and column 8 to the next line. So the result will be something like this: 
223445 BG2A093.x1    51    7     51    4 1    75    96    0 1    0    
+44
223446 BG2A073.x1    51    7     51    4 2    75    95    0 1    0   4
+3 
223447 BG2A033.x1    51    7     51    4 1    44    92    0 1    0    
+42
223448 BG2A693.x1    51    7     51    4 1    45    93    1 1    0    
+43
223449 BG2A045.x1    51    7     51    4 1    47    95    1 1    0    
+47
223501 BG2A034.x1    51    7     51    4 2    47    95    0 1    0    
+46
223442 BG2A021.x1    51    7     51    4 1    48    96    0 1    0    
+45

[download]
I've try some perl scripts and came up something like this: 
#!/usr/local/bin/perl -w 
my $pre_ref_pos_b;
my $pre_ref_pos_e;
my $count

while (<>) {

   chomp;
   my ($r_no,$r_name,$r_len,$r_pos_b, $r_pos_e, $ref_seq_no, $ref_pos_
+b, $ref_pos_e, $rev, $no_match, $paired, $aln_score) = split;
   while (defined($pre_ref_pos_b) && defined($pre_ref_pos_e) eq $ref_p
+os_b && $ref_pos_e) {
   $count++;
   print $r_name,$count,$r_ref_pos_b,$ref_pos_e\n;
   }
   $pre_ref_pos_b = $ref_pos_b;
   $pre_ref_pos_e = $ref_pos_e;

  }
}

[download]
The problem is I've no idea how the lines of data being kept in the memory, and how should I put in the program so that it will reset the count whenever the the ref_pos_b and ref_pos_e is different from the proceeding lines. Your help is really appreciate, I'm learning the perl, and I'm still very very new to it. Best regads.

In reply to Compute previous lines data by joomanji

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