update functions on handling other modification bases #134
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I modified read.modkit() function to handle other modification calls based on users' choice. If present, other modifications bases can be either drop, or added to the methylation matrix, or added to the coverage matrix, or stored as a separate matrix. I created a modified class "BSseq_mod" to store information (including methylation, unmethylation, other modification) if users chose to store other modification bases as a separate matrix. Relevant functions (hasBeenSmoothed_mod, getBSseq_mod, strandCollapse_mod, getMeth_mod, getCoverage_mod, chrSelectBSseq_mod, orderBSseq_mod) are constructed for class "BSseq_mod".
Also, the test data for read.modkit now contains chromosome 21 and 22 with top 1000 CpGs.