update functions on handling other modification bases #137
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I modified read.modkit() function to handle other modification calls. When other modification bases are called by modkit, the same position has two rows of information regarding to each modification. read.modkit() function removes redundant information and creates a Bsseq object with "M" matrix representing 5mc + 5hmc, and "Cov" matrix represent 5mc + 5hmc + unmodified bases.