I guess Easiest way is to show you what my data looks like in simpler way bp = basepair I have data of different chromosomes with start and end point of cluster tags in each of chromosomes it looks like : 
columns = 1: chr  2: start 3:end 4: info(X) 5: info(X) 6:strand 

chr1    101  105   X     X     -
chr1    102  108   X     X     -
chr1    106  111   X     X     -
chr1    112  113   X     X     -
chr1    113  115   X     X     -
chr2    114  118   X     X     -  
chr2    119  121   X     X     -
chr2    120  123   X     X    -
chr3    125  130   X     X    -
chr3    131  132   X     X   -

I need column 1 - 2 -3 - 6 

I want to count the overlappes with 2 basepair overlappes for each cor
+dinates in each chromosome and give ID number for those over laps tog
+ether like in chr1 there are 4 cordinates and 3 of them have overlapp
+ed 
except the last cordinate  : so I will need to first count those 3 ove
+rlappes 
and give them ID_1 then ID_2 will give to last cordinate in chr1 which
+ is not have overlapped with others .
then Counting is became zero for the chr2 and check inside the chr2 co
+rdinates for overlap and give ID from ID_1 for chr2 again and countin
+g and so on for all chromosomes and give the out put like this :

TSSD_ID        chr       start        end      strand      count
  ID_1         1          101          111       -           3
  ID_2         1          112          113       -           1
  ID_3         1          113          115       -           1
  ID_1         2          114          118       -           1   
  ID_2         2          119          123       -           2 
  ID_1         3          125          132       -           1

[download]
this the output I want to get but Mine is not working well !

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

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