Documentation code blocks

[SimonGreenhill]

The code blocks included in the docs are sometimes missing the leading ">" e.g.

library("BAMMtools")

instead of

> library("BAMMtools")

This should be one or the other. without a leading > has the benefit of being easier to cut and paste into R.

[drabosky]

for consistency with sweave style, please preface lines of R code with ">" in documentation