Adapt likelihood functions to MethylCounts and update test, manuals, and examples (alpha version). #154
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Merge Kaspers update to workflows with Srens updates to likelihood functions
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I've also added function to get coverage from getMethylCounts by adding M+U and H. I will have a look at the flexibility of read.bedMethyl() and check if it always returns a H matrix where the entries are 0 when no H calls are present in bedMethyl file.