fix bug in parsing of paired FASTA files

call to .good() was always on the first read file, which meant that the
last line of the second (aka right reads) FASTA file wasn't being read,
so reading pairs of FASTA files would fail at the end.  Fix is to call
.good() on the P->inOut->readIn[imate] instead.
Merge branch 'master' of github.com:parolfe/STAR