Fail when R1 reads > R2 reads

[andreazauli]

It seems the software stops to work ad exit when number of R1 reads is greater then number of R2.
The error is because in fastq-lib.cpp qual.n returns -1 for the last record of the second file you pass :
if (fq->qual.n <= 0)
return 0;
and then with other reads it consequently fails.
But when R1 is lower, we still have -1, for reads 2, but the cycle stops and the error disappear.

When R1 reads is greater then number of R2, if you exchange the file in the command line, it works again.

If you have time...
Thank you.
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