Shell Programming and Scripting

Hey fellas,
I wrote an script which its output is like this:

Code:

a 1 T
a 1 T 
a 2 A 
b 5 G
b 5 G
b 5 G

I wanna print $1 $2 and the total number of $2 value as the third column and after that $3. Sth like this:

Code:

a 1 2 T
a 2 1 A
b 5 3 G

I know how to do it with a given input file but cannot do it using pipe.

It would be more cool if you can help to have the output like this: (to have zero value for those which are missed)

Code:

a 1 2 T
a 2 1 A 
- 3 0 - 
- 4 0 - 
b 5 3 G

But this last step is not that important. just for fun though!
Thanks for your help.

I don't understand. How are you doing this with a regular file? What is it about the processing you're doing that makes it hard to do the same thing on a pipe? (Is there some reason why you need to perform a seek operation on the input? That is something you can't do on a pipe.)

Will you ever have input like:

Code:

a 1 F
a 1 T
b 1 T

with the same values for $2 but different values for $1 and/or $3? If so, when are they supposed to be combined and what values are supposed to be printed for $1 and $4?

Try a for loop for the intermediate values, for example:

Code:

awk '
  p q !=$1 $2{
    if(p)print p,q,t,v
    t=1
    for(i=q+1; i<$2; i++)
      printf "- %s 0 -\n", i
    p=$1
    q=$2
    v=$3
    next
  }
  {
    t++
  } 
  END{
    print p,q,t,v
  }' infile

Tnx Don Cragun for your consideration.
I am working with huge bam files which I need to parse and do some analysis on them. Since they are so huge and I'm not expert in programming I analyse them step by stem and using pipe function to go to next step.
The data that I have so far has 4 column which the first column is just two different values for all lines. what I wanna do is to report the second column and the number of its repeats in a separate column. and then the corresponding value on 4th column which is the same for similar values in column 2.

I managed to do it by using two scripts. I'm just wondering if its possible to do in one single script. So Then I can use the output I have so far as an input using pipe.
Thanks.

---------- Post updated at 05:29 PM ---------- Previous update was at 05:26 PM ----------

Thanks Scrutinizer
I haven't applied what you wrote yet. But it needs an input file right? Is it possible to modify it to be able to use this script for the output of another script as I mentioned?
The only thing I know to do such things like that is pipe function. If there is any other way let me know plz.
Thanks

Leave off 'infile' and awk will read from standard input instead.