Move "using namespace std" after #includes
Move "using namespace std" after #includes

...so that namespace "std" already exists when we try to use it,
as it will have been declared by the standard headers #included.
Doing otherwise elicits a warning from Clang.

arq5x/bedtools2,arq5x/bedtools2,jmarshall/bedtools2,arq5x/bedtools2,jmarshall/bedtools2,jmarshall/bedtools2,jmarshall/bedtools2,jmarshall/bedtools2,arq5x/bedtools2,arq5x/bedtools2