.callbinary {Rbowtie2} | R Documentation

## Make system call for binaries

### Description

Function that makes a system call for the bowtie binaries. Note it is not intended to be used outside of the package.

### Usage

    .callbinary(
      bin1,
      args1,
      op = NULL,
      bin2 = NULL,
      args2 = NULL,
      path = NULL,
      lang = NULL
    )

### Arguments

`bin1` | `Character`. The binary used for the system call.
`args1` | `Character`. The arguments to pass to the binary.
`op` | `Character`. Optional: Generally used if needed to pipe to another binary.
`bin2` | `Character`. Optional: Another binary that can be used in the system call. Generally the output of the first binary is piped to the this binary.
`args2` | `Character` Optional: The arguments to pass to the second binary.
`path` | `Character` Optional: If passed to function, returns the path. Needed for Rsamtools to convert from sam to bam.
`lang` | `Character`. The interpreter used to execute the binary

### Value

The output of the system call or the path provided.

### Author(s)

Zheng Wei

[Package Rbowtie2 version 2.0.0 Index]