.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]