TSSD_ID     Chr              Start                  End      Count    
+ Strand 
ID_1      chr21      9417056      9417076 1      -  
ID_2      chr21      9417667      9417687 1      -  
ID_3      chr21      9512082      9512102 2      -  
ID_3      chr21      9512082      9512102 2      -  
ID_5      chr21      9535321      9535341 1      -  
ID_6      chr21      9540527      9540547 1      -  
ID_7      chr21      9544899      9544919 1      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      - 
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_8      chr21      9564970      9564990 48      -  
ID_56      chr21      9575389      9575409 1      -  
ID_57      chr21      9652071      9652091 1      -  
ID_58      chr21      9671166      9671186 3      -  
ID_58      chr21      9671166      9671186 3      -  
ID_58      chr21      9671166      9671186 3      -  
ID_61      chr21      9700592      9700612 1      -  
ID_62      chr21      9704082      9704102 1      -  
ID_63      chr21      9705333      9705353 1      -

[download]
if you look at the first column the ID number is jumping from 2 to 5 and from 8 to 52 as you see it adds the counting the column 5 to the ID ! but I dont want it to do that ! I want to add +1 to ID number when the entries in column three (start column) for example 1st entry - 2nd entry > 2 and add +1 to column5 when 1st entry - 2nd entry < 2 (in column 3 (start) ) I mean for entry and the next entry and give me unique output instead of printing for many times like : 
TSSD_ID     Chr              Start                  End      Count    
+ Strand 
ID_1      chr21      9417056      9417076 1      -  
ID_2      chr21      9417667      9417687 1      -  
ID_3      chr21      9512081      9512102 1      -  
ID_3      chr21      9512082      9512102 3      -  
ID_3      chr21      9512083      9512104 1      -  
ID_3      chr21      9512085      9512120 1      -  
ID_5      chr21      9535321      9535341 1      -  
ID_6      chr21      9540527      9540547 1      -  
ID_7      chr21      9544899      9544919 1      -  
ID_8      chr21      9564970      9564990 1      -  
ID_8      chr21      9564975      9564993 2      -  
ID_9      chr21      9564970      9564990 8      -  
ID_10      chr21      9564970      9564990 4      -  
ID_11     chr21      9564970      9564990 7      -

[download]
as you see in ID_3 in one line count is 3 which I means at that position there are three identical clusters again in ID_3 there are some with counting 1 which are in that area and covered in 2bp but are not same like this : 
|=====|
|=====|      there are identical in ID_3 and count as 3
|=====|
        |=====|
               |=====|  and these two are again 
                                 in ID_3 but there are not
                                 Identical so they have different
                           counting as each of them count as one!
and 
when 
|=====|
             |=====|    they do not have 2bp overlap
                                 the ID will change to ID_4
as you see in ID_3 all of them had 2bp overlapped

[download]

In reply to Re^2: Help the counting! by g-alone
in thread Help the counting! by g-alone

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