bowtie2-build crashes if a contig is all 'n'

[samhunter]

With the recent implementation of repeat masking, it is now possible to get a contig which looks like this:

masked nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

When bowtie2-build is called on a file containing a contig like this, it will crash: * glibc detected * bowtie2-build: double free or corruption (out): 0x000000000481b210 ***

Solution: Avoid writing out any cotings which are all 'n' (these won't recruit reads anyway).