htsjdk.samtools.util

Class ProcessExecutor

java.lang.Object

htsjdk.samtools.util.ProcessExecutor

public class ProcessExecutor
extends java.lang.Object

Utility class that will execute sub processes via Runtime.getRuntime().exec(...) and read off the output from stderr and stdout of the sub process. This implementation uses a different thread to read each stream: the current thread for stdout and another, internal thread for stderr. This utility is able to handle concurrent executions, spawning as many threads as are required to handle the concurrent load.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ProcessExecutor.ExitStatusAndOutput

Constructor Summary

Constructors

Constructor and Description
ProcessExecutor()

Method Summary

Modifier and Type	Method and Description
static int	execute(java.lang.String command) Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
static int	execute(java.lang.String[] commandParts) Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
static int	execute(java.lang.String[] commandParts, java.lang.String outputStreamString) Executes the command via Runtime.getRuntime().exec(), writes outputStreamString to the process output stream if it is not null, then writes stderr to log.error and stdout to log.info and blocks until the command is complete.
static ProcessExecutor.ExitStatusAndOutput	executeAndReturnInterleavedOutput(java.lang.String command) Execute the command and capture stdout and stderr.
static ProcessExecutor.ExitStatusAndOutput	executeAndReturnInterleavedOutput(java.lang.String[] commandArray) Execute the command and capture stdout and stderr.
static java.lang.String	executeAndReturnResult(java.lang.String command)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProcessExecutor

public ProcessExecutor()

Method Detail

execute

public static int execute(java.lang.String command)

Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.

Parameters:

command - command string

Returns:

return code of command

See Also:

Runtime.exec(String)

execute

public static int execute(java.lang.String[] commandParts)

Executes the command via Runtime.getRuntime().exec() then writes stderr to log.error and stdout to log.info and blocks until the command is complete.

Parameters:

commandParts - command string

Returns:

return code of command

See Also:

Runtime.exec(String[])

execute

public static int execute(java.lang.String[] commandParts,
                          java.lang.String outputStreamString)

Executes the command via Runtime.getRuntime().exec(), writes outputStreamString to the process output stream if it is not null, then writes stderr to log.error and stdout to log.info and blocks until the command is complete.

Parameters:

commandParts - command string

Returns:

return code of command

See Also:

Runtime.exec(String[])

executeAndReturnResult

public static java.lang.String executeAndReturnResult(java.lang.String command)

executeAndReturnInterleavedOutput

public static ProcessExecutor.ExitStatusAndOutput executeAndReturnInterleavedOutput(java.lang.String command)

Execute the command and capture stdout and stderr.

Returns:

Exit status of command, and both stderr and stdout interleaved into stdout attribute.

executeAndReturnInterleavedOutput

public static ProcessExecutor.ExitStatusAndOutput executeAndReturnInterleavedOutput(java.lang.String[] commandArray)

Execute the command and capture stdout and stderr.

Returns:

Exit status of command, and both stderr and stdout interleaved into stdout attribute.