Added Haplotify option to allpaths plu various improvments

Allpaths is run with option Haplotify (personal communication with allpaths developers, it dramatically improves assembly connectivity)
run validation now reads options form yaml files rather than assuming a predefined folder specification

just as a recommendation, you shouldn't use the word ```file``` as a variable name. It is a [python built-in type](https://docs.python.org/2/library/stdtypes.html#file-objects), so you're overwriting it.