AlleleProfileR.parsetrailseq: Parse the trailing sequence in a chimeric pair

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

Description

Worker function to process the trailing sequence of a chimeric pair.

Usage

AlleleProfileR.parsetrailseq(obj, gene, cutoff.large, index, input_atg,
  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.
input_atg	If TRUE, ATG is destroyed in the lead sequence
cutrangelist	cutrangelist

Value

List with elements: output_fs, output_sm, output_lg, dels, list(ins_loc,ins_bps), indelseq, output_utr, output_inrange

Author(s)

Arne Bruyneel

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