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Removed custom '<clipN>'
cs
notation.
Instead of writing a script to process the '<clipN>' notation, I decided to stick with just using tuples to designate features that have clipping. This makes counting mutations and clipping easier.
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dcdb543
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We can chat about this this afternoon, but I think simply keeping
cs
strings with clipping as tuples inparse_alignment_cs
makes more sense than adding in clipping, which we'll just process away in downstream functions anyway. It makes theparse_alignment_cs
dataframe a bit less easy to look at, but most users won't use that dataframe anyway.