You need to remove vector<string> fullSequence, sequenceNames;
in the void Sequence::fastaRead
function. When you define those variables inside that function and use them, you are not accessing the ones in the class that have the same name, you are accessing the local variables that you have defined in that function, unless you prepend them with this->
while accessing.
The variables in the class are actually empty and you get a segmentation fault.