.hisat2Bin {Rhisat2}R Documentation

Call the HISAT2 binary with additional arguments.

Description

Adapted from the Rbowtie package

Usage

.hisat2Bin(bin = c("hisat2", "hisat2-build"), args = "", execute = TRUE)

Arguments

bin

The name of the binary, either hisat2 or hisat2-build.

args

A character string containing the arguments that will be passed to the binary.

execute

Logical scalar, whether to execute the command. If FALSE, return a string with the shell command.

Value

If execute is TRUE, returns the console output of running the hisat2 command. If execute is FALSE, returns the shell command.


[Package Rhisat2 version 1.8.0 Index]