support long reads in -amos option

Link: https://github.com/sebhtml/ray/issues/162
Link: https://github.com/sebhtml/ray/issues/163
Link: http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/594
Link: https://raw.github.com/sebhtml/patches/master/ray/Ray-v2.2.0-fix-for-amos-and-long-reads.patch
Link: http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/602
Reported-by: Bastian Hornung <bastian.hornung@wur.nl>
Tested-by: Bastian Hornung <bastian.hornung@wur.nl>
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>