Surveyor: fix endless loop while reading scaffolds

If a scaffold was given as entry to GenomeAssemblyReader and
the gap was 3 full lines of N, then the SequenceKmerReader
entered into an infinite loop.
Also fix when there is a trailing empty line in the fasta file
in entry: GenomeAssemblyReader won't try to store the kmer.

Signed-off-by: Maxime Déraspe <maximilien1er@gmail.com>
Surveyor: renamed the option to write kmer matrix to "-write-kmer-matrix"

Used to be "-run-kmer-matrix"

Signed-off-by: Maxime Déraspe <maximilien1er@gmail.com>
Merge branch 'fix-assembly-reader' of https://github.com/Zorino/ray.git