get_bowtie2_cmd: Wrapper to build up the Bowtie2 command

In jkruppa/virDisco: Modules for a viral detection pipeline

Description

Wrapper function to build up the Bowtie2 command for the the system() call

Usage

get_bowtie2_cmd(inFile, samOutFile, referenceDir, method, p = 32,
  all = FALSE)

Arguments

inFile	File path to the in file(s)
samOutFile	Path to the sam output file
referenceDir	Path to the reference dir
method	Should ene-to-end or lcal mapping be used?
p	Number of used cores
all	Shoul the reads mapped to all possible positions on the reference [default = FALSE]

Details

This function is running internally in the map_dna_ref.

Value

character

Author(s)

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.