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1,WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
...
3,WG0045068-DNA,C01,0,102186_C01_WTCCCT519805,...
1,WG0045066-DNA,A01,0,102176_A01_WTCCCT527545,...
2,WG0045066-DNA,B01,0,102176_B01_WTCCCT527498,...

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WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
WG0045068-DNA,B01,0,102186_B01_WTCCCT519793,...
...
3,WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
1,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
2,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...

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open (FILE1, "<", "filein.txt") || die "$!";
open (FILE2, ">", "fileout.out") || die "$!";
...
4,WG0045068-DNA,C01,0,102186_C11_WTCCCT519805,...

not sorted, but sorting should not be a problem :)

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```
input.file
102186
102176
```

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open (FILEIN, "<", "input.file") || die "$!";
...
  $counter->{$_} = 0;
}
close FILEIN;

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elsif($output eq "Inhouse") {
         
...
                
 ...