htsjdk.beta.plugin

Class IOUtils

java.lang.Object

htsjdk.beta.plugin.IOUtils

public class IOUtils
extends java.lang.Object

Class for updated IOUtils methods that use either IOPath Path in public method argument lists.

Constructor Summary

Constructors

Constructor and Description
IOUtils()

Method Summary

Modifier and Type	Method and Description
static IOPath	createTempPath(java.lang.String prefix, java.lang.String suffix) Create a temporary file using a given name prefix and name suffix and return a Path.
static java.lang.String	getStringFromPath(IOPath ioPath) Get the entire contents of an IOPath as a string.
static HtsPath	toHtsPath(java.nio.file.Path toConvert) Convert Path to GATKPath, returning null if input was null.
static void	writeStringToPath(IOPath ioPath, java.lang.String contents, boolean gzipOutput) Write a String to an IOPath.

Methods inherited from class java.lang.Object

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

Constructor Detail

IOUtils

public IOUtils()

Method Detail

createTempPath

public static IOPath createTempPath(java.lang.String prefix,
                                    java.lang.String suffix)

Create a temporary file using a given name prefix and name suffix and return a Path.

Parameters:

prefix -

suffix -

Returns:

temp File that will be deleted on exit

Throws:

java.io.IOException

toHtsPath

public static HtsPath toHtsPath(java.nio.file.Path toConvert)

Convert Path to GATKPath, returning null if input was null.

Parameters:

toConvert - Path to convert to GATKPath

Returns:

a Path, or null if the input was null.

getStringFromPath

public static java.lang.String getStringFromPath(IOPath ioPath)

Get the entire contents of an IOPath as a string.

Parameters:

ioPath -

Returns:

a UTF-8 string representation of the file contents

writeStringToPath

public static void writeStringToPath(IOPath ioPath,
                                     java.lang.String contents,
                                     boolean gzipOutput)

Write a String to an IOPath.

Parameters:

ioPath - path where contents should be written

contents - a UTF-8 string to be written

gzipOutput - if true, gzip output