.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 1.99.1 Index]