Allow for different methilation patterns for different combinations on enzymes

[anpefi]

From a mail from He Zinqing:

The origin MSAP protocol uses isoesquizomeric endonucleases HpaII and MspI, but I use Tfi I/Pfe I in our study according to the paper Stable Epigenetic Variants Selected from an Induced Hypomethylated Fragaria vesca Population (Jihua Xu et al. 2016, in the attachment). So in our study, Tfi I/Pfe patterns are: (1/1: unmethylation; 1/0: hemimethylation; 0/0: methylation; 0/1: missing data). It is different from HPA/MSP patterns, so we can’t use R package msap.

This a thing to study and it would be a great addition

[anpefi]

Done. I have to check that anything is broken and also change the manual accordingly, but it is almost ready to merge into the develop branch.