for my $c (0..$#AbsFiles){
        my $key1=undef; 
        my $key2=undef; 
        if ($AbsFiles[$c] =~ /R2_001\.fastq$/){
           open INPUT1 ... ; 
           ...stuff to set key1; 
           close INPUT1; 
           }
        if ($AbsFiles[$c] =~ /R1_001\.fastq$/$/){
           open INPUT2 ... ; 
           ...stuff to set key2; 
           close INPUT2; 
           }
        if (defined($key1) && defined($key2} && key1 eq $key2 ) { 
          ... stuff to do when both are set and equal ... 
          } 
        else { 
           ...stuff to do otherwise .. 
          } 
        } # c