gr.isclip: Check if reads are clipped

gr.isclipR Documentation

Check if reads are clipped

Description

Returns a logical vector of length of the input GRanges that that classifies a read as clipped or not. The user can specify a cutoff value for how many bases need to be clipped.

Usage

gr.isclip(gr, clip.cutoff = 10)

Arguments

gr

Granges OR data.table that has cigar field and qname field

clip.cutoff

Minimum number of bases that are clipped to call the reads as clipped

Value

logical of length of input, denoting whether that read is part of a clipped read pair.


mskilab/skitools documentation built on July 5, 2024, 7:27 a.m.