Two hotfixes: runtime error when -m and -s specified for a PE lib (with no MP contamination obviously).
Empty repeat file in rare cases when --separate_repeats specified and no scaffolding is performed with an existing second library.
 Bumped up version number to 1.1.2.
Fixed runtime error bug for PE lib and empty repeat.fa file bug
Merge branch 'hotfix/1.1.1'