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fragment id  index 
accb     10  A
bbc      11  B
ccd      12  C

fragment id index
ccd      15   D     
llk      11   B
kks      12   C

fragment  id_file file 1   id_file2      file 2
accb         10      1                    0
...
ccd          12      1       15           1   
llk                  0       11           1
kks                  0       12           1

use strict;
use warnings;
...
print OUT (sort keys %hash);
close OUT;