Fix read.bedMethyl when strandCollapse=F and add alpha version of read.bedMethyl for output="MethylCounts" #153
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kasperdanielhansen merged 5 commits intohansenlab:develfrom Nov 4, 2025
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…ndCollapse = F bug
…ct. Default is still a BSseq object and is not modified in this commit
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Fix bug in read.bedMethyl when strandCollapse=F and prepare function for unstranded input. Change assay name in objects imported by read.bedMethyl from C to U for canonical/unmethylated cytosine.
Add argument output to read.bedMethyl to specify if files should be imported as BSseq object (default) or MethylCounts. - The default BSseq object imported is still a "false" BSseq object with M,H,C,D and Cov assays.