Create a function read.modkit to read in methyl Bed files created by modkit to Bsseq object

[yixuan-chen-elisa]

A function read.modkit() is created to read in methyl bed files and construct Bsseq objects. When N_other_mod (number of reads that pass thresholds and where modification is different from the listed base) are all zeros, we constructed one BSseq object, and it’s pretty similar to how we construct BSseq objects using read.modbam2bed(). When there are non-zero N_other_mod reads, N_other_mod and its corresponding coverage, cov_other_mod are stored in addition to N_mod and its corresponding coverage. Two Bsseq objects are constructed with the first one having N_mod as methylation, N_mod + N_canonical as coverage and the second one having N_other_mod as methylation, N_other_mod + N_canonical as coverage.