GRanges Not Great for Variant Storage

Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.

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Open DarioS opened 4 years ago

DarioS commented 4 years ago

Storing the variants as VRanges instead of GRanges allows cleaner code to be written. For example

snps.indel[nchar(snps.indel$REF) > 1 | nchar(snps.indel$ALT) > 1]

could be better written as

variants[isIndel(variants)]

Could the next version switch to VRanges?