AlleleProfileR.parseleadseq: Parse the lead sequence in a chimeric pair

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function processes the leading sequence in a chimeric pair.

Usage

AlleleProfileR.parseleadseq(obj, gene, cutoff.large, index, cutrangelist)

Arguments

obj	Row in the BAM datatable, a sequencing read.
gene	Gene information vector
cutoff.large	Cutoff value for determining whether an indel is large or small. Default is 25.
index	Path to the .fa file containing the reference genome.
cutrangelist	cutrangelist

Value

List with elements: output_fs, output_sm, output_lg, dels, list(ins_loc,ins_bps), startpos+atgpos-1, indelseq, output_utr, output_atg, output_inrange

Author(s)

Arne Bruyneel

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.