org.broadinstitute.hellbender.utils.io

Class IOUtils

java.lang.Object

org.broadinstitute.hellbender.utils.io.IOUtils

public final class IOUtils
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
IOUtils()

Method Summary

Modifier and Type	Method and Description
static void	assertFileIsReadable(java.nio.file.Path path)
static void	canReadFile(java.io.File... files) Checks that one or more user provided files are in fact regular (i.e.
static void	createDirectory(java.lang.String pathString) Creates a directory, in local FS, HDFS, or Google buckets to write individual files in.
static java.io.File	createTempDir(java.lang.String prefix) Creates a temp directory with the given prefix.
static java.io.File	createTempFile(java.lang.String name, java.lang.String extension) Creates a temp file that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
static java.io.File	createTempFileInDirectory(java.lang.String name, java.lang.String extension, java.io.File targetDir) Creates a temp file in a target directory that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
static void	deleteRecursivelyOnExit(java.io.File dir) Schedule a file or directory to be deleted on jvm exit.
static java.nio.file.Path	getPath(java.lang.String uriString) Converts the given URI to a Path object.
static void	gunzip(java.io.File input, java.io.File output) Un-gzips the input file to the output file.
static java.io.File	gunzipToTempIfNeeded(java.io.File maybeGzipedFile) Un-gzips the input file to a output file but only if the file's name ends with '.gz'.
static boolean	isBamFileName(java.lang.String inputFileName) Returns true if the file's extension is BAM.
static boolean	isCramFile(java.io.File inputFile) Returns true if the file's extension is CRAM.
static boolean	isCramFile(java.nio.file.Path path) Returns true if the file's extension is CRAM.
static boolean	isCramFileName(java.lang.String inputFileName) Returns true if the file's extension is CRAM.
static boolean	isSpecialFile(java.io.File file) Returns true if the file is a special file.
static java.io.PrintStream	makePrintStreamMaybeGzipped(java.io.File file) Makes a print stream for a file, gzipping on the fly if the file's name ends with '.gz'.
static java.io.Reader	makeReaderMaybeGzipped(java.io.File file) Makes a reader for a file, unzipping if the file's name ends with '.gz'.
static java.io.Reader	makeReaderMaybeGzipped(java.io.InputStream in, boolean zipped) makes a reader for an inputStream wrapping it in an appropriate unzipper if necessary
static java.io.InputStream	makeZippedInputStream(java.io.InputStream in) creates an input stream from a zipped stream
static byte[]	readFileIntoByteArray(java.io.File source) Reads the entirety of the given file into a byte array.
static byte[]	readFileIntoByteArray(java.io.File source, int readBufferSize) Reads the entirety of the given file into a byte array using the requested read buffer size.
static byte[]	readStreamIntoByteArray(java.io.InputStream in, int readBufferSize) Reads all data from the given stream into a byte array using the requested read buffer size.
static java.io.File	replaceExtension(java.io.File file, java.lang.String extension)
static java.lang.String	replaceExtension(java.lang.String path, java.lang.String extension)
static boolean	tryDelete(java.io.File file) Tries to delete a file.
static java.lang.String	urlDecode(java.lang.String string)
static java.lang.String	urlEncode(java.lang.String string)
static void	writeByteArrayToFile(byte[] bytes, java.io.File destination) Writes the given array of bytes to a file
static void	writeByteArrayToStream(byte[] bytes, java.io.OutputStream out) Writes the given array of bytes to a stream
static void	writeResource(Resource resource, java.io.File file) Writes the an embedded resource to a file.
static java.io.File	writeTempFile(java.lang.String content, java.lang.String prefix, java.lang.String suffix) Writes content to a temp file and returns the path to the temporary file.
static java.io.File	writeTempFile(java.lang.String content, java.lang.String prefix, java.lang.String suffix, java.io.File directory) Writes content to a temp file and returns the path to the temporary file.
static java.io.File	writeTempResource(Resource resource) Writes an embedded resource to a temporary file.
static java.io.File	writeTempResourceFromPath(java.lang.String resourcePath, java.lang.Class<?> relativeClass) Create a resource from a path and a relative class, and write it to a temporary file.

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

isCramFile

public static boolean isCramFile(java.io.File inputFile)

Returns true if the file's extension is CRAM.

isCramFile

public static boolean isCramFile(java.nio.file.Path path)

Returns true if the file's extension is CRAM.

isCramFileName

public static boolean isCramFileName(java.lang.String inputFileName)

Returns true if the file's extension is CRAM.

isBamFileName

public static boolean isBamFileName(java.lang.String inputFileName)

Returns true if the file's extension is BAM.

createTempDir

public static java.io.File createTempDir(java.lang.String prefix)

Creates a temp directory with the given prefix. The directory and any contents will be automatically deleted at shutdown. This will not work if the temp dir is not representable as a File.

Parameters:

prefix - Prefix for the directory name.

Returns:

The created temporary directory.

writeTempFile

public static java.io.File writeTempFile(java.lang.String content,
                                         java.lang.String prefix,
                                         java.lang.String suffix)

Writes content to a temp file and returns the path to the temporary file.

Parameters:

content - to write.

prefix - Prefix for the temp file.

suffix - Suffix for the temp file.

Returns:

the path to the temp file.

writeTempFile

public static java.io.File writeTempFile(java.lang.String content,
                                         java.lang.String prefix,
                                         java.lang.String suffix,
                                         java.io.File directory)

Writes content to a temp file and returns the path to the temporary file.

Parameters:

content - to write.

prefix - Prefix for the temp file.

suffix - Suffix for the temp file.

directory - Directory for the temp file.

Returns:

the path to the temp file.

isSpecialFile

public static boolean isSpecialFile(java.io.File file)

Returns true if the file is a special file.

Parameters:

file - File path to check.

Returns:

true if the file is a special file.

tryDelete

public static boolean tryDelete(java.io.File file)

Tries to delete a file. Emits a warning if the file is not a special file and was unable to be deleted.

Parameters:

file - File to delete.

Returns:

true if the file was deleted.

writeTempResource

public static java.io.File writeTempResource(Resource resource)

Writes an embedded resource to a temporary file. The temporary file is automatically scheduled for deletion on exit.

Parameters:

resource - Embedded resource.

Returns:

the temporary file containing the contents of the resource, which is automatically scheduled for deletion on exit.

writeTempResourceFromPath

public static java.io.File writeTempResourceFromPath(java.lang.String resourcePath,
                                                     java.lang.Class<?> relativeClass)

Create a resource from a path and a relative class, and write it to a temporary file. If the relative class is null then the system classloader will be used and the path must be absolute. The temporary file is automatically scheduled for deletion on exit.

Parameters:

resourcePath - Relative or absolute path to the class.

relativeClass - Relative class to use as a class loader and for a relative package.

Returns:

a temporary file containing the contents of the resource, which is automatically scheduled for deletion on exit.

writeResource

public static void writeResource(Resource resource,
                                 java.io.File file)

Writes the an embedded resource to a file. File is not scheduled for deletion and must be cleaned up by the caller.

Parameters:

resource - Embedded resource.

file - File path to write.

readFileIntoByteArray

public static byte[] readFileIntoByteArray(java.io.File source)

Reads the entirety of the given file into a byte array. Uses a read buffer size of 4096 bytes.

Parameters:

source - File to read

Returns:

The contents of the file as a byte array

readFileIntoByteArray

public static byte[] readFileIntoByteArray(java.io.File source,
                                           int readBufferSize)

Reads the entirety of the given file into a byte array using the requested read buffer size.

Parameters:

source - File to read

readBufferSize - Number of bytes to read in at one time

Returns:

The contents of the file as a byte array

readStreamIntoByteArray

public static byte[] readStreamIntoByteArray(java.io.InputStream in,
                                             int readBufferSize)

Reads all data from the given stream into a byte array using the requested read buffer size.

Parameters:

in - Stream to read data from

readBufferSize - Number of bytes to read in at one time

Returns:

The contents of the stream as a byte array

writeByteArrayToFile

public static void writeByteArrayToFile(byte[] bytes,
                                        java.io.File destination)

Writes the given array of bytes to a file

Parameters:

bytes - Data to write

destination - File to write the data to

writeByteArrayToStream

public static void writeByteArrayToStream(byte[] bytes,
                                          java.io.OutputStream out)

Writes the given array of bytes to a stream

Parameters:

bytes - Data to write

out - Stream to write the data to

gunzip

public static void gunzip(java.io.File input,
                          java.io.File output)

Un-gzips the input file to the output file.

gunzipToTempIfNeeded

public static java.io.File gunzipToTempIfNeeded(java.io.File maybeGzipedFile)

Un-gzips the input file to a output file but only if the file's name ends with '.gz'. In this case the new temp file is masked for deletion on exit and returned from this method. Otherwise, that is if the argument is not a gzipped file, this method just returns the argument.

makeReaderMaybeGzipped

public static java.io.Reader makeReaderMaybeGzipped(java.io.File file)
                                             throws java.io.IOException

Makes a reader for a file, unzipping if the file's name ends with '.gz'.

Throws:

java.io.IOException

makeReaderMaybeGzipped

public static java.io.Reader makeReaderMaybeGzipped(java.io.InputStream in,
                                                    boolean zipped)
                                             throws java.io.IOException

makes a reader for an inputStream wrapping it in an appropriate unzipper if necessary

Parameters:

zipped - is this stream zipped

Throws:

java.io.IOException

makeZippedInputStream

public static java.io.InputStream makeZippedInputStream(java.io.InputStream in)
                                                 throws java.io.IOException

creates an input stream from a zipped stream

Returns:

tries to create a block gzipped input stream and if it's not block gzipped it produces to a gzipped stream instead

Throws:

java.util.zip.ZipException - if !in.markSupported()

java.io.IOException

makePrintStreamMaybeGzipped

public static java.io.PrintStream makePrintStreamMaybeGzipped(java.io.File file)
                                                       throws java.io.IOException

Makes a print stream for a file, gzipping on the fly if the file's name ends with '.gz'.

Throws:

java.io.IOException

createTempFile

public static java.io.File createTempFile(java.lang.String name,
                                          java.lang.String extension)

Creates a temp file that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.

Parameters:

name - Prefix of the file.

extension - Extension to concat to the end of the file.

Returns:

A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.

createTempFileInDirectory

public static java.io.File createTempFileInDirectory(java.lang.String name,
                                                     java.lang.String extension,
                                                     java.io.File targetDir)

Creates a temp file in a target directory that will be deleted on exit This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.

Parameters:

name - Prefix of the file.

extension - Extension to concat to the end of the file name.

targetDir - Directory in which to create the temp file. If null, the default temp directory is used.

Returns:

A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.

replaceExtension

public static java.lang.String replaceExtension(java.lang.String path,
                                                java.lang.String extension)

Parameters:

extension - a file extension, may include 0 or more leading dots which will be replaced with a single dot

Returns:

replace the final extension on a path with the given extension

replaceExtension

public static java.io.File replaceExtension(java.io.File file,
                                            java.lang.String extension)

deleteRecursivelyOnExit

public static void deleteRecursivelyOnExit(java.io.File dir)

Schedule a file or directory to be deleted on jvm exit. This will silently delete the directory as well as it's contents. It improves upon FileUtils.forceDeleteOnExit(java.io.File) by deleting directories and files that did not exist at call time.

Parameters:

dir - to be deleted

getPath

public static java.nio.file.Path getPath(java.lang.String uriString)

Converts the given URI to a Path object. If the filesystem cannot be found in the usual way, then attempt to load the filesystem provider using the thread context classloader. This is needed when the filesystem provider is loaded using a URL classloader (e.g. in spark-submit). Also makes an attempt to interpret the argument as a file name if it's not a URI.

Parameters:

uriString - the URI to convert.

Returns:

the resulting Path

Throws:

UserException - if an I/O error occurs when creating the file system

assertFileIsReadable

public static void assertFileIsReadable(java.nio.file.Path path)

Parameters:

path - Path to test

Throws:

UserException.CouldNotReadInputFile - if the file isn't readable and a regular file

canReadFile

public static void canReadFile(java.io.File... files)

Checks that one or more user provided files are in fact regular (i.e. not a directory or a special device) readable files.

Parameters:

files - the input files to test.

Throws:

java.lang.IllegalArgumentException - if any input file file is null or files is null.

UserException - if any file is not a regular file or it cannot be read.

createDirectory

public static void createDirectory(java.lang.String pathString)
                            throws java.io.IOException

Creates a directory, in local FS, HDFS, or Google buckets to write individual files in.

Throws:

java.io.IOException

urlEncode

public static final java.lang.String urlEncode(java.lang.String string)

urlDecode

public static final java.lang.String urlDecode(java.lang.String string)