java.lang.Object
- htsjdk.samtools.util.IOUtil

```
public class IOUtil
extends Object
```
Miscellaneous stateless static IO-oriented methods. Also used for utility methods that wrap or aggregate functionality in Java IO.

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`BCF_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.BCF` instead.
`static Set<String>`	`BLOCK_COMPRESSED_EXTENSIONS`	Deprecated. Use since June 2019 `FileExtensions.BLOCK_COMPRESSED` instead.
`static String`	`COMPRESSED_VCF_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.COMPRESSED_VCF` instead.
`static String`	`COMPRESSED_VCF_INDEX_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.COMPRESSED_VCF_INDEX` instead.
`static String`	`DICT_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.DICT` instead.
`static long`	`FIVE_GBS`
`static int`	`GZIP_HEADER_READ_LENGTH`	number of bytes that will be read for the GZIP-header in the function `isGZIPInputStream(InputStream)`
`static String`	`INTERVAL_LIST_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.INTERVAL_LIST` instead.
`static long`	`ONE_GB`
`static String`	`SAM_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.SAM` instead.
`static int`	`STANDARD_BUFFER_SIZE`	Deprecated. Use `Defaults.NON_ZERO_BUFFER_SIZE` instead.
`static long`	`TWO_GBS`
`static String[]`	`VCF_EXTENSIONS`	Deprecated. since June 2019 Use `FileExtensions.VCF_LIST` instead.
`static List<String>`	`VCF_EXTENSIONS_LIST`	Deprecated. since June 2019 Use `FileExtensions.VCF_LIST` instead.
`static String`	`VCF_FILE_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.VCF` instead.
`static String`	`VCF_INDEX_EXTENSION`	Deprecated. since June 2019 Use `FileExtensions.VCF_INDEX` instead.

Constructor Summary

Constructors
Constructor Description

IOUtil()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static Path`	`addExtension(Path path, String extension)`	Adds the extension to the given path.
`static void`	`assertDirectoryIsReadable(File dir)`	Checks that a directory is non-null, extent, readable and a directory otherwise a runtime exception is thrown.
`static void`	`assertDirectoryIsWritable(File dir)`	Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
`static void`	`assertDirectoryIsWritable(Path dir)`	Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
`static void`	`assertFileIsReadable(File file)`	Checks that a file is non-null, exists, is not a directory and is readable.
`static void`	`assertFileIsReadable(Path path)`	Checks that a file is non-null, exists, is not a directory and is readable.
`static void`	`assertFileIsWritable(File file)`	Checks that a file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
`static void`	`assertFilesAreReadable(List<File> files)`	Checks that each file is non-null, exists, is not a directory and is readable.
`static void`	`assertFilesAreWritable(List<File> files)`	Checks that each file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable.
`static void`	`assertFilesEqual(File f1, File f2)`	Checks that the two files are the same length, and have the same content, otherwise throws a runtime exception.
`static void`	`assertFileSizeNonZero(File file)`	Checks that a file is of non-zero length
`static void`	`assertInputIsValid(String input)`	Checks that an input is is non-null, a URL or a file, exists, and if its a file then it is not a directory and is readable.
`static void`	`assertInputsAreValid(List<String> inputs)`	Checks that each string is non-null, exists or is a URL, and if it is a file then not a directory and is readable.
`static void`	`assertPathsAreReadable(List<Path> paths)`	Checks that each path is non-null, exists, is not a directory and is readable.
`static String`	`basename(File f)`	Returns the name of the file minus the extension (i.e.
`static void`	`copyDirectoryTree(File fileOrDirectory, File destination)`	Copies a directory tree (all subdirectories and files) recursively to a destination
`static void`	`copyFile(File input, File output)`	Copy input to output, overwriting output if it already exists.
`static void`	`copyStream(InputStream input, OutputStream output)`	Utility method to copy the contents of input to output.
`static File`	`createTempDir(String prefix, String suffix)`	Create a temporary subdirectory in the default temporary-file directory, using the given prefix and suffix to generate the name.
`static boolean`	`deleteDirectoryTree(File fileOrDirectory)`	Delete the given file or directory.
`static void`	`deleteFiles(File... files)`	Delete a list of files, and write a warning message if one could not be deleted.
`static void`	`deleteFiles(Iterable<File> files)`
`static void`	`deleteOnExit(Path path)`	Register a `Path` for deletion on JVM exit.
`static void`	`deletePath(Path path)`	Attempt to delete a single path and log an error if it is not deleted.
`static void`	`deletePaths(Iterable<Path> paths)`	Iterate through Paths and delete each one.
`static void`	`deletePaths(Path... paths)`
`static List<Path>`	`filesToPaths(Collection<File> files)`	Takes a list of Files and converts them to a list of Paths Runs .toPath() on the contents of the input.
`static String`	`fileSuffix(File f)`	Returns the name of the file extension (i.e.
`static int`	`getCompressionLevel()`
`static File`	`getDefaultTmpDir()`	Returns a default tmp directory.
`static Path`	`getDefaultTmpDirPath()`	Returns a default tmp directory as a Path.
`static File[]`	`getFilesMatchingRegexp(File directory, String regexp)`
`static File[]`	`getFilesMatchingRegexp(File directory, Pattern regexp)`
`static String`	`getFullCanonicalPath(File file)`	Returns the full path to the file with all symbolic links resolved
`static Path`	`getPath(String uriString)`	Converts the given URI to a `Path` object.
`static List<Path>`	`getPaths(List<String> uriStrings)`
`static boolean`	`hasBlockCompressedExtension(File file)`	Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
`static boolean`	`hasBlockCompressedExtension(String fileName)`	Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
`static boolean`	`hasBlockCompressedExtension(URI uri)`	Checks if a file ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
`static boolean`	`hasBlockCompressedExtension(Path path)`	Checks if a path ends in one of the `FileExtensions.BLOCK_COMPRESSED`.
`static boolean`	`hasGzipFileExtension(Path path)`	check if the file name ends with .gz, .gzip, or .bfq
`static boolean`	`hasScheme(String uriString)`	Check if the given URI has a scheme.
`static boolean`	`isBlockCompressed(Path path)`	Checks if the provided path is block-compressed (including extension).
`static boolean`	`isBlockCompressed(Path path, boolean checkExtension)`	Checks if the provided path is block-compressed.
`static boolean`	`isGZIPInputStream(InputStream stream)`	Test whether a input stream looks like a GZIP input.
`static boolean`	`isRegularPath(File file)`
`static boolean`	`isRegularPath(Path path)`
`static boolean`	`isUrl(String input)`	Returns true iff the string is a url.
`static String`	`makeFileNameSafe(String str)`	Takes a string and replaces any characters that are not safe for filenames with an underscore
`static SeekableStream`	`maybeBufferedSeekableStream(SeekableStream stream)`
`static SeekableStream`	`maybeBufferedSeekableStream(SeekableStream stream, int bufferSize)`
`static SeekableStream`	`maybeBufferedSeekableStream(File file)`
`static SeekableStream`	`maybeBufferedSeekableStream(URL url)`
`static InputStream`	`maybeBufferInputStream(InputStream is)`
`static InputStream`	`maybeBufferInputStream(InputStream is, int bufferSize)`
`static OutputStream`	`maybeBufferOutputStream(OutputStream os)`
`static OutputStream`	`maybeBufferOutputStream(OutputStream os, int bufferSize)`
`static Reader`	`maybeBufferReader(Reader reader)`
`static Reader`	`maybeBufferReader(Reader reader, int bufferSize)`
`static Writer`	`maybeBufferWriter(Writer writer)`
`static Writer`	`maybeBufferWriter(Writer writer, int bufferSize)`
`static File`	`newTempFile(String prefix, String suffix, File[] tmpDirs)`	Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
`static File`	`newTempFile(String prefix, String suffix, File[] tmpDirs, long minBytesFree)`	Creates a new tmp file on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
`static Path`	`newTempPath(String prefix, String suffix, Path[] tmpDirs)`	Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
`static Path`	`newTempPath(String prefix, String suffix, Path[] tmpDirs, long minBytesFree)`	Creates a new tmp path on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
`static BufferedReader`	`openFileForBufferedReading(File file)`	Checks that a file exists and is readable, and then returns a buffered reader for it.
`static BufferedReader`	`openFileForBufferedReading(Path path)`	Checks that a path exists and is readable, and then returns a buffered reader for it.
`static BufferedReader`	`openFileForBufferedUtf8Reading(File file)`	Opens a file for reading, decompressing it if necessary
`static BufferedWriter`	`openFileForBufferedUtf8Writing(File file)`	Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
`static BufferedWriter`	`openFileForBufferedUtf8Writing(Path path)`	Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
`static BufferedWriter`	`openFileForBufferedWriting(File file)`	Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
`static BufferedWriter`	`openFileForBufferedWriting(File file, boolean append)`	Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
`static BufferedWriter`	`openFileForBufferedWriting(Path path, OpenOption... openOptions)`	Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
`static OutputStream`	`openFileForMd5CalculatingWriting(File file)`
`static OutputStream`	`openFileForMd5CalculatingWriting(Path file)`
`static InputStream`	`openFileForReading(File file)`	Opens a file for reading, decompressing it if necessary
`static InputStream`	`openFileForReading(Path path)`	Opens a file for reading, decompressing it if necessary
`static OutputStream`	`openFileForWriting(File file)`	Opens a file for writing, overwriting the file if it already exists
`static OutputStream`	`openFileForWriting(File file, boolean append)`	Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
`static OutputStream`	`openFileForWriting(Path path, OpenOption... openOptions)`	Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
`static InputStream`	`openGzipFileForReading(File file)`	Opens a GZIP-encoded file for reading, decompressing it if necessary
`static InputStream`	`openGzipFileForReading(Path path)`	Opens a GZIP-encoded file for reading, decompressing it if necessary
`static OutputStream`	`openGzipFileForWriting(File file, boolean append)`	Opens a GZIP encoded file for writing
`static OutputStream`	`openGzipFileForWriting(Path path, OpenOption... openOptions)`	Opens a GZIP encoded file for writing
`static String`	`readFully(InputStream in)`	Reads everything from an input stream as characters and returns a single String.
`static IterableOnceIterator<String>`	`readLines(File f)`	Returns an iterator over the lines in a text file.
`static void`	`recursiveDelete(Path directory)`	Delete a directory and all files in it.
`static void`	`setCompressionLevel(int compressionLevel)`	Sets the GZip compression level for subsequent GZIPOutputStream object creation.
`static long`	`sizeOfTree(File fileOrDirectory)`	Returns the size (in bytes) of the file or directory and all it's children.
`static String`	`slurp(File file)`	Convenience overload for `slurp(java.io.InputStream, java.nio.charset.Charset)` using the default charset `Charset.defaultCharset()`.
`static String`	`slurp(InputStream is)`	Convenience overload for `slurp(java.io.InputStream, java.nio.charset.Charset)` using the default charset `Charset.defaultCharset()`.
`static String`	`slurp(InputStream is, Charset charSet)`	Reads all of the stream into a String, decoding with the provided `Charset` then closes the stream quietly.
`static List<String>`	`slurpLines(File file)`	Returns all of the untrimmed lines in the provided file.
`static List<String>`	`slurpLines(InputStream is)`
`static BufferedInputStream`	`toBufferedStream(InputStream stream)`	Wrap the given stream in a BufferedInputStream, if it isn't already wrapper
`static Path`	`toPath(File fileOrNull)`
`static void`	`transferByStream(InputStream in, OutputStream out, long bytes)`	Transfers from the input stream to the output stream using stream operations and a buffer.
`static List<File>`	`unrollFiles(Collection<File> inputs, String... extensions)`	Go through the files provided and if they have one of the provided file extensions pass the file into the output otherwise assume that file is a list of filenames and unfold it into the output.
`static List<Path>`	`unrollPaths(Collection<Path> inputs, String... extensions)`	Go through the files provided and if they have one of the provided file extensions pass the file to the output otherwise assume that file is a list of filenames and unfold it into the output (recursively).

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - STANDARD_BUFFER_SIZE
```
@Deprecated
public static final int STANDARD_BUFFER_SIZE
```
    Deprecated.
    Use Defaults.NON_ZERO_BUFFER_SIZE instead.
  - ONE_GB
```
public static final long ONE_GB
```
    See Also:
    
    Constant Field Values
  - TWO_GBS
```
public static final long TWO_GBS
```
    See Also:
    
    Constant Field Values
  - FIVE_GBS
```
public static final long FIVE_GBS
```
    See Also:
    
    Constant Field Values
  - VCF_FILE_EXTENSION
```
@Deprecated
public static final String VCF_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.VCF instead.
    
    See Also:
    
    Constant Field Values
  - VCF_INDEX_EXTENSION
```
@Deprecated
public static final String VCF_INDEX_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.VCF_INDEX instead.
    
    See Also:
    
    Constant Field Values
  - BCF_FILE_EXTENSION
```
@Deprecated
public static final String BCF_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.BCF instead.
    
    See Also:
    
    Constant Field Values
  - COMPRESSED_VCF_FILE_EXTENSION
```
@Deprecated
public static final String COMPRESSED_VCF_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.COMPRESSED_VCF instead.
    
    See Also:
    
    Constant Field Values
  - COMPRESSED_VCF_INDEX_EXTENSION
```
@Deprecated
public static final String COMPRESSED_VCF_INDEX_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.COMPRESSED_VCF_INDEX instead.
    
    See Also:
    
    Constant Field Values
  - VCF_EXTENSIONS_LIST
```
@Deprecated
public static final List<String> VCF_EXTENSIONS_LIST
```
    Deprecated.
    since June 2019 Use FileExtensions.VCF_LIST instead.
  - VCF_EXTENSIONS
```
@Deprecated
public static final String[] VCF_EXTENSIONS
```
    Deprecated.
    since June 2019 Use FileExtensions.VCF_LIST instead.
    
    Possible extensions for VCF files and related formats.
  - INTERVAL_LIST_FILE_EXTENSION
```
@Deprecated
public static final String INTERVAL_LIST_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.INTERVAL_LIST instead.
    
    See Also:
    
    Constant Field Values
  - SAM_FILE_EXTENSION
```
@Deprecated
public static final String SAM_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.SAM instead.
    
    See Also:
    
    Constant Field Values
  - DICT_FILE_EXTENSION
```
@Deprecated
public static final String DICT_FILE_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.DICT instead.
    
    See Also:
    
    Constant Field Values
  - BLOCK_COMPRESSED_EXTENSIONS
```
@Deprecated
public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS
```
    Deprecated.
    Use since June 2019 FileExtensions.BLOCK_COMPRESSED instead.
  - GZIP_HEADER_READ_LENGTH
```
public static final int GZIP_HEADER_READ_LENGTH
```
    number of bytes that will be read for the GZIP-header in the function isGZIPInputStream(InputStream)
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - IOUtil
```
public IOUtil()
```
- Method Detail
  - setCompressionLevel
```
public static void setCompressionLevel(int compressionLevel)
```
    Sets the GZip compression level for subsequent GZIPOutputStream object creation.
    
    Parameters:
    
    compressionLevel - 0 <= compressionLevel <= 9
  - getCompressionLevel
```
public static int getCompressionLevel()
```
  - toBufferedStream
```
public static BufferedInputStream toBufferedStream(InputStream stream)
```
    Wrap the given stream in a BufferedInputStream, if it isn't already wrapper
    
    Parameters:
    
    stream - stream to be wrapped
    
    Returns:
    
    A BufferedInputStream wrapping stream, or stream itself if stream instanceof BufferedInputStream.
  - transferByStream
```
public static void transferByStream(InputStream in,
                                    OutputStream out,
                                    long bytes)
```
    Transfers from the input stream to the output stream using stream operations and a buffer.
  - maybeBufferOutputStream
```
public static OutputStream maybeBufferOutputStream(OutputStream os)
```
    Returns:
    
    If Defaults.BUFFER_SIZE > 0, wrap os in BufferedOutputStream, else return os itself.
  - maybeBufferOutputStream
```
public static OutputStream maybeBufferOutputStream(OutputStream os,
                                                   int bufferSize)
```
    Returns:
    
    If bufferSize > 0, wrap os in BufferedOutputStream, else return os itself.
  - maybeBufferedSeekableStream
```
public static SeekableStream maybeBufferedSeekableStream(SeekableStream stream,
                                                         int bufferSize)
```
  - maybeBufferedSeekableStream
```
public static SeekableStream maybeBufferedSeekableStream(SeekableStream stream)
```
  - maybeBufferedSeekableStream
```
public static SeekableStream maybeBufferedSeekableStream(File file)
```
  - maybeBufferedSeekableStream
```
public static SeekableStream maybeBufferedSeekableStream(URL url)
```
  - maybeBufferInputStream
```
public static InputStream maybeBufferInputStream(InputStream is)
```
    Returns:
    
    If Defaults.BUFFER_SIZE > 0, wrap is in BufferedInputStream, else return is itself.
  - maybeBufferInputStream
```
public static InputStream maybeBufferInputStream(InputStream is,
                                                 int bufferSize)
```
    Returns:
    
    If bufferSize > 0, wrap is in BufferedInputStream, else return is itself.
  - maybeBufferReader
```
public static Reader maybeBufferReader(Reader reader,
                                       int bufferSize)
```
  - maybeBufferReader
```
public static Reader maybeBufferReader(Reader reader)
```
  - maybeBufferWriter
```
public static Writer maybeBufferWriter(Writer writer,
                                       int bufferSize)
```
  - maybeBufferWriter
```
public static Writer maybeBufferWriter(Writer writer)
```
  - deleteFiles
```
public static void deleteFiles(File... files)
```
    Delete a list of files, and write a warning message if one could not be deleted.
    
    Parameters:
    
    files - Files to be deleted.
  - deleteFiles
```
public static void deleteFiles(Iterable<File> files)
```
  - deletePaths
```
public static void deletePaths(Path... paths)
```
  - deletePaths
```
public static void deletePaths(Iterable<Path> paths)
```
    Iterate through Paths and delete each one. Note: Path is itself an Iterable. This method special cases that and deletes the single Path rather than Iterating the Path for targets to delete.
    
    Parameters:
    
    paths - an iterable of Paths to delete
  - deletePath
```
public static void deletePath(Path path)
```
    Attempt to delete a single path and log an error if it is not deleted.
  - isRegularPath
```
public static boolean isRegularPath(File file)
```
    Returns:
    
    true if the path is not a device (e.g. /dev/null or /dev/stdin), and is not an existing directory. I.e. is is a regular path that may correspond to an existing file, or a path that could be a regular output file.
  - isRegularPath
```
public static boolean isRegularPath(Path path)
```
    Returns:
    
    true if the path is not a device (e.g. /dev/null or /dev/stdin), and is not an existing directory. I.e. is is a regular path that may correspond to an existing file, or a path that could be a regular output file.
  - newTempFile
```
public static File newTempFile(String prefix,
                               String suffix,
                               File[] tmpDirs,
                               long minBytesFree)
                        throws IOException
```
    Creates a new tmp file on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
    
    Throws:
    
    IOException
  - newTempFile
```
public static File newTempFile(String prefix,
                               String suffix,
                               File[] tmpDirs)
                        throws IOException
```
    Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
    
    Throws:
    
    IOException
  - getDefaultTmpDir
```
public static File getDefaultTmpDir()
```
    Returns a default tmp directory.
  - newTempPath
```
public static Path newTempPath(String prefix,
                               String suffix,
                               Path[] tmpDirs,
                               long minBytesFree)
                        throws IOException
```
    Creates a new tmp path on one of the available temp filesystems, registers it for deletion on JVM exit and then returns it.
    
    Throws:
    
    IOException
  - newTempPath
```
public static Path newTempPath(String prefix,
                               String suffix,
                               Path[] tmpDirs)
                        throws IOException
```
    Creates a new tmp file on one of the potential filesystems that has at least 5GB free.
    
    Throws:
    
    IOException
  - getDefaultTmpDirPath
```
public static Path getDefaultTmpDirPath()
```
    Returns a default tmp directory as a Path.
  - deleteOnExit
```
public static void deleteOnExit(Path path)
```
    Register a Path for deletion on JVM exit.
    
    See Also:
    
    DeleteOnExitPathHook
  - basename
```
public static String basename(File f)
```
    Returns the name of the file minus the extension (i.e. text after the last "." in the filename).
  - assertInputIsValid
```
public static void assertInputIsValid(String input)
```
    Checks that an input is is non-null, a URL or a file, exists, and if its a file then it is not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    input - the input to check for validity
  - isUrl
```
public static boolean isUrl(String input)
```
    Returns true iff the string is a url. Helps distinguish url inputs form file path inputs.
  - assertFileIsReadable
```
public static void assertFileIsReadable(File file)
```
    Checks that a file is non-null, exists, is not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    file - the file to check for readability
  - assertFileIsReadable
```
public static void assertFileIsReadable(Path path)
```
    Checks that a file is non-null, exists, is not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    path - the file to check for readability
  - assertFilesAreReadable
```
public static void assertFilesAreReadable(List<File> files)
```
    Checks that each file is non-null, exists, is not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    files - the list of files to check for readability
  - assertPathsAreReadable
```
public static void assertPathsAreReadable(List<Path> paths)
```
    Checks that each path is non-null, exists, is not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    paths - the list of paths to check for readability
  - assertInputsAreValid
```
public static void assertInputsAreValid(List<String> inputs)
```
    Checks that each string is non-null, exists or is a URL, and if it is a file then not a directory and is readable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    inputs - the list of files to check for readability
  - assertFileIsWritable
```
public static void assertFileIsWritable(File file)
```
    Checks that a file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    file - the file to check for writability
  - assertFilesAreWritable
```
public static void assertFilesAreWritable(List<File> files)
```
    Checks that each file is non-null, and is either extent and writable, or non-existent but that the parent directory exists and is writable. If any condition is false then a runtime exception is thrown.
    
    Parameters:
    
    files - the list of files to check for writability
  - assertDirectoryIsWritable
```
public static void assertDirectoryIsWritable(File dir)
```
    Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
    
    Parameters:
    
    dir - the dir to check for writability
  - assertDirectoryIsWritable
```
public static void assertDirectoryIsWritable(Path dir)
```
    Checks that a directory is non-null, extent, writable and a directory otherwise a runtime exception is thrown.
    
    Parameters:
    
    dir - the dir to check for writability
  - assertDirectoryIsReadable
```
public static void assertDirectoryIsReadable(File dir)
```
    Checks that a directory is non-null, extent, readable and a directory otherwise a runtime exception is thrown.
    
    Parameters:
    
    dir - the dir to check for writability
  - assertFilesEqual
```
public static void assertFilesEqual(File f1,
                                    File f2)
```
    Checks that the two files are the same length, and have the same content, otherwise throws a runtime exception.
  - assertFileSizeNonZero
```
public static void assertFileSizeNonZero(File file)
```
    Checks that a file is of non-zero length
  - openFileForReading
```
public static InputStream openFileForReading(File file)
```
    Opens a file for reading, decompressing it if necessary
    
    Parameters:
    
    file - The file to open
    
    Returns:
    
    the input stream to read from
  - openFileForReading
```
public static InputStream openFileForReading(Path path)
```
    Opens a file for reading, decompressing it if necessary
    
    Parameters:
    
    path - The file to open
    
    Returns:
    
    the input stream to read from
  - openGzipFileForReading
```
public static InputStream openGzipFileForReading(File file)
```
    Opens a GZIP-encoded file for reading, decompressing it if necessary
    
    Parameters:
    
    file - The file to open
    
    Returns:
    
    the input stream to read from
  - openGzipFileForReading
```
public static InputStream openGzipFileForReading(Path path)
```
    Opens a GZIP-encoded file for reading, decompressing it if necessary
    
    Parameters:
    
    path - The file to open
    
    Returns:
    
    the input stream to read from
  - openFileForWriting
```
public static OutputStream openFileForWriting(File file)
```
    Opens a file for writing, overwriting the file if it already exists
    
    Parameters:
    
    file - the file to write to
    
    Returns:
    
    the output stream to write to
  - openFileForWriting
```
public static OutputStream openFileForWriting(File file,
                                              boolean append)
```
    Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
    
    Parameters:
    
    file - the file to write to
    
    append - whether to append to the file if it already exists (we overwrite it if false)
    
    Returns:
    
    the output stream to write to
  - openFileForWriting
```
public static OutputStream openFileForWriting(Path path,
                                              OpenOption... openOptions)
```
    Opens a file for writing, gzip it if it ends with ".gz" or "bfq"
    
    Parameters:
    
    path - the file to write to
    
    openOptions - options to use when opening the file
    
    Returns:
    
    the output stream to write to
  - hasGzipFileExtension
```
public static boolean hasGzipFileExtension(Path path)
```
    check if the file name ends with .gz, .gzip, or .bfq
  - openFileForBufferedWriting
```
public static BufferedWriter openFileForBufferedWriting(File file,
                                                        boolean append)
```
    Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
  - openFileForBufferedWriting
```
public static BufferedWriter openFileForBufferedWriting(Path path,
                                                        OpenOption... openOptions)
```
    Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
  - openFileForBufferedWriting
```
public static BufferedWriter openFileForBufferedWriting(File file)
```
    Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
  - openFileForBufferedUtf8Writing
```
public static BufferedWriter openFileForBufferedUtf8Writing(File file)
```
    Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
  - openFileForBufferedUtf8Writing
```
public static BufferedWriter openFileForBufferedUtf8Writing(Path path)
```
    Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error
  - openFileForBufferedUtf8Reading
```
public static BufferedReader openFileForBufferedUtf8Reading(File file)
```
    Opens a file for reading, decompressing it if necessary
    
    Parameters:
    
    file - The file to open
    
    Returns:
    
    the input stream to read from
  - openGzipFileForWriting
```
public static OutputStream openGzipFileForWriting(File file,
                                                  boolean append)
```
    Opens a GZIP encoded file for writing
    
    Parameters:
    
    file - the file to write to
    
    append - whether to append to the file if it already exists (we overwrite it if false)
    
    Returns:
    
    the output stream to write to
  - openGzipFileForWriting
```
public static OutputStream openGzipFileForWriting(Path path,
                                                  OpenOption... openOptions)
```
    Opens a GZIP encoded file for writing
    
    Parameters:
    
    path - the file to write to
    
    openOptions - options to control how the file is opened
    
    Returns:
    
    the output stream to write to
  - openFileForMd5CalculatingWriting
```
public static OutputStream openFileForMd5CalculatingWriting(File file)
```
  - openFileForMd5CalculatingWriting
```
public static OutputStream openFileForMd5CalculatingWriting(Path file)
```
  - copyStream
```
public static void copyStream(InputStream input,
                              OutputStream output)
```
    Utility method to copy the contents of input to output. The caller is responsible for opening and closing both streams.
    
    Parameters:
    
    input - contents to be copied
    
    output - destination
  - copyFile
```
public static void copyFile(File input,
                            File output)
```
    Copy input to output, overwriting output if it already exists.
  - getFilesMatchingRegexp
```
public static File[] getFilesMatchingRegexp(File directory,
                                            String regexp)
```
    Parameters:
    
    directory -
    
    regexp -
    
    Returns:
    
    list of files matching regexp.
  - getFilesMatchingRegexp
```
public static File[] getFilesMatchingRegexp(File directory,
                                            Pattern regexp)
```
  - deleteDirectoryTree
```
public static boolean deleteDirectoryTree(File fileOrDirectory)
```
    Delete the given file or directory. If a directory, all enclosing files and subdirs are also deleted.
  - sizeOfTree
```
public static long sizeOfTree(File fileOrDirectory)
```
    Returns the size (in bytes) of the file or directory and all it's children.
  - copyDirectoryTree
```
public static void copyDirectoryTree(File fileOrDirectory,
                                     File destination)
```
    Copies a directory tree (all subdirectories and files) recursively to a destination
  - createTempDir
```
public static File createTempDir(String prefix,
                                 String suffix)
```
    Create a temporary subdirectory in the default temporary-file directory, using the given prefix and suffix to generate the name. Note that this method is not completely safe, because it create a temporary file, deletes it, and then creates a directory with the same name as the file. Should be good enough.
    
    Parameters:
    
    prefix - The prefix string to be used in generating the file's name; must be at least three characters long
    
    suffix - The suffix string to be used in generating the file's name; may be null, in which case the suffix ".tmp" will be used
    
    Returns:
    
    File object for new directory
  - openFileForBufferedReading
```
public static BufferedReader openFileForBufferedReading(File file)
```
    Checks that a file exists and is readable, and then returns a buffered reader for it.
  - openFileForBufferedReading
```
public static BufferedReader openFileForBufferedReading(Path path)
```
    Checks that a path exists and is readable, and then returns a buffered reader for it.
  - makeFileNameSafe
```
public static String makeFileNameSafe(String str)
```
    Takes a string and replaces any characters that are not safe for filenames with an underscore
  - fileSuffix
```
public static String fileSuffix(File f)
```
    Returns the name of the file extension (i.e. text after the last "." in the filename) including the .
  - getFullCanonicalPath
```
public static String getFullCanonicalPath(File file)
```
    Returns the full path to the file with all symbolic links resolved
  - readFully
```
public static String readFully(InputStream in)
```
    Reads everything from an input stream as characters and returns a single String.
  - readLines
```
public static IterableOnceIterator<String> readLines(File f)
```
    Returns an iterator over the lines in a text file. The underlying resources are automatically closed when the iterator hits the end of the input, or manually by calling close().
    
    Parameters:
    
    f - a file that is to be read in as text
    
    Returns:
    
    an iterator over the lines in the text file
  - slurpLines
```
public static List<String> slurpLines(File file)
                               throws FileNotFoundException
```
    Returns all of the untrimmed lines in the provided file.
    
    Throws:
    
    FileNotFoundException
  - slurpLines
```
public static List<String> slurpLines(InputStream is)
                               throws FileNotFoundException
```
    Throws:
    
    FileNotFoundException
  - slurp
```
public static String slurp(File file)
                    throws FileNotFoundException
```
    Convenience overload for slurp(java.io.InputStream, java.nio.charset.Charset) using the default charset Charset.defaultCharset().
    
    Throws:
    
    FileNotFoundException
  - slurp
```
public static String slurp(InputStream is)
```
    Convenience overload for slurp(java.io.InputStream, java.nio.charset.Charset) using the default charset Charset.defaultCharset().
  - slurp
```
public static String slurp(InputStream is,
                           Charset charSet)
```
    Reads all of the stream into a String, decoding with the provided Charset then closes the stream quietly.
  - unrollFiles
```
public static List<File> unrollFiles(Collection<File> inputs,
                                     String... extensions)
```
    Go through the files provided and if they have one of the provided file extensions pass the file into the output otherwise assume that file is a list of filenames and unfold it into the output.
  - unrollPaths
```
public static List<Path> unrollPaths(Collection<Path> inputs,
                                     String... extensions)
```
    Go through the files provided and if they have one of the provided file extensions pass the file to the output otherwise assume that file is a list of filenames and unfold it into the output (recursively).
  - hasScheme
```
public static boolean hasScheme(String uriString)
```
    Check if the given URI has a scheme.
    
    Parameters:
    
    uriString - the URI to check
    
    Returns:
    
    true if the given URI has a scheme, false if not, or if the URI is malformed.
  - getPath
```
public static Path getPath(String uriString)
                    throws IOException
```
    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).
    
    Parameters:
    
    uriString - the URI to convert
    
    Returns:
    
    the resulting Path
    
    Throws:
    
    IOException - an I/O error occurs creating the file system
  - getPaths
```
public static List<Path> getPaths(List<String> uriStrings)
                           throws RuntimeIOException
```
    Throws:
    
    RuntimeIOException
  - toPath
```
public static Path toPath(File fileOrNull)
```
  - filesToPaths
```
public static List<Path> filesToPaths(Collection<File> files)
```
    Takes a list of Files and converts them to a list of Paths Runs .toPath() on the contents of the input.
    
    Parameters:
    
    files - a List of Files to convert to Paths
    
    Returns:
    
    a new List containing the results of running toPath on the elements of the input
  - isGZIPInputStream
```
public static boolean isGZIPInputStream(InputStream stream)
```
    Test whether a input stream looks like a GZIP input. This identifies both gzip and bgzip streams as being GZIP.
    
    Parameters:
    
    stream - the input stream.
    
    Returns:
    
    true if `stream` starts with a gzip signature.
    
    Throws:
    
    IllegalArgumentException - if `stream` cannot mark or reset the stream
  - addExtension
```
public static Path addExtension(Path path,
                                String extension)
```
    Adds the extension to the given path.
    
    Parameters:
    
    path - the path to start from, eg. "/folder/file.jpg"
    
    extension - the extension to add, eg. ".bak"
    
    Returns:
    
    "/folder/file.jpg.bak"
  - isBlockCompressed
```
public static boolean isBlockCompressed(Path path,
                                        boolean checkExtension)
                                 throws IOException
```
    Checks if the provided path is block-compressed.
    Note that using checkExtension=true would avoid the cost of opening the file, but if hasBlockCompressedExtension(String) returns false this would not detect block-compressed files such BAM.
    
    Parameters:
    
    path - file to check if it is block-compressed.
    
    checkExtension - if true, checks the extension before opening the file.
    
    Returns:
    
    true if the file is block-compressed; false otherwise.
    
    Throws:
    
    IOException - if there is an I/O error.
  - isBlockCompressed
```
public static boolean isBlockCompressed(Path path)
                                 throws IOException
```
    Checks if the provided path is block-compressed (including extension).
    Note that block-compressed file extensions FileExtensions.BLOCK_COMPRESSED are not checked by this method.
    
    Parameters:
    
    path - file to check if it is block-compressed.
    
    Returns:
    
    true if the file is block-compressed; false otherwise.
    
    Throws:
    
    IOException - if there is an I/O error.
  - hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(String fileName)
```
    Checks if a file ends in one of the FileExtensions.BLOCK_COMPRESSED.
    
    Parameters:
    
    fileName - string name for the file. May be an HTTP/S url.
    
    Returns:
    
    true if the file has a block-compressed extension; false otherwise.
  - hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(Path path)
```
    Checks if a path ends in one of the FileExtensions.BLOCK_COMPRESSED.
    
    Parameters:
    
    path - object to extract the name from.
    
    Returns:
    
    true if the path has a block-compressed extension; false otherwise.
  - hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(File file)
```
    Checks if a file ends in one of the FileExtensions.BLOCK_COMPRESSED.
    
    Parameters:
    
    file - object to extract the name from.
    
    Returns:
    
    true if the file has a block-compressed extension; false otherwise.
  - hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(URI uri)
```
    Checks if a file ends in one of the FileExtensions.BLOCK_COMPRESSED.
    
    Parameters:
    
    uri - file as an URI.
    
    Returns:
    
    true if the file has a block-compressed extension; false otherwise.
  - recursiveDelete
```
public static void recursiveDelete(Path directory)
```
    Delete a directory and all files in it.
    
    Parameters:
    
    directory - The directory to be deleted (along with its subdirectories)

Class IOUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STANDARD_BUFFER_SIZE

ONE_GB

TWO_GBS

FIVE_GBS

VCF_FILE_EXTENSION

VCF_INDEX_EXTENSION

BCF_FILE_EXTENSION

COMPRESSED_VCF_FILE_EXTENSION

COMPRESSED_VCF_INDEX_EXTENSION

VCF_EXTENSIONS_LIST

VCF_EXTENSIONS

INTERVAL_LIST_FILE_EXTENSION

SAM_FILE_EXTENSION

DICT_FILE_EXTENSION

BLOCK_COMPRESSED_EXTENSIONS

GZIP_HEADER_READ_LENGTH

Constructor Detail

IOUtil

Method Detail

setCompressionLevel

getCompressionLevel

toBufferedStream

transferByStream

maybeBufferOutputStream

maybeBufferOutputStream

maybeBufferedSeekableStream

maybeBufferedSeekableStream

maybeBufferedSeekableStream

maybeBufferedSeekableStream

maybeBufferInputStream

maybeBufferInputStream

maybeBufferReader

maybeBufferReader

maybeBufferWriter

maybeBufferWriter

deleteFiles

deleteFiles

deletePaths

deletePaths

deletePath

isRegularPath

isRegularPath

newTempFile

newTempFile

getDefaultTmpDir

newTempPath

newTempPath

getDefaultTmpDirPath

deleteOnExit

basename

assertInputIsValid

isUrl

assertFileIsReadable

assertFileIsReadable

assertFilesAreReadable

assertPathsAreReadable

assertInputsAreValid

assertFileIsWritable

assertFilesAreWritable

assertDirectoryIsWritable

assertDirectoryIsWritable

assertDirectoryIsReadable

assertFilesEqual

assertFileSizeNonZero

openFileForReading

openFileForReading

openGzipFileForReading

openGzipFileForReading

openFileForWriting

openFileForWriting

openFileForWriting

hasGzipFileExtension

openFileForBufferedWriting

openFileForBufferedWriting