Class SamInputResource

Method Details

• toString

  public String toString()

  Overrides:

  toString in class Object

• of

  public static SamInputResource of(File file)

  Creates a SamInputResource reading from the provided resource, with no index.

• of

  public static SamInputResource of(Path path)

  Creates a SamInputResource reading from the provided resource, with no index.

• of

  public static SamInputResource of(Path path, Function<SeekableByteChannel,SeekableByteChannel> wrapper)

  Creates a SamInputResource reading from the provided resource, with no index, and with a wrapper to apply to the SeekableByteChannel for custom prefetching/buffering.

• of

  public static SamInputResource of(InputStream inputStream)

  Creates a SamInputResource reading from the provided resource, with no index.

• of

  public static SamInputResource of(URL url)

  Creates a SamInputResource reading from the provided resource, with no index.

• of

  public static SamInputResource of(SeekableStream seekableStream)

  Creates a SamInputResource reading from the provided resource, with no index.

• of

  public static SamInputResource of(SRAAccession acc)

• of

  public static SamInputResource of(URI uri)

  Creates a SamInputResource from a URI which may represent an htsget path, or some other resource such as a filesystem path or a URL, with no index. This method will first attempt to treat the resource as an htsget resource, then fall back to treating it as a file system path, then as a URL

• of

  public static SamInputResource of(URI uri, Function<SeekableByteChannel,SeekableByteChannel> wrapper)

  Creates a SamInputResource with no index from a URI which may represent an htsget path, or some other resource such as a filesystem path or a URL, with no index, and with a wrapper to apply to the SeekableByteChannel for custom prefetching/buffering. This method will first attempt to treat the resource as an htsget resource, then fall back to treating it as a file system path, then as a URL

• of

  public static SamInputResource of(String string)

  Creates a SamInputResource from a string specifying *either* a url or a file path

• index

  public SamInputResource index(File file)

  Updates the index to point at the provided resource, then returns itself.

• index

  public SamInputResource index(Path path)

  Updates the index to point at the provided resource, then returns itself.

• index

  public SamInputResource index(Path path, Function<SeekableByteChannel,SeekableByteChannel> wrapper)

  Updates the index to point at the provided resource, with the provided wrapper, then returns itself.

• index

  public SamInputResource index(InputStream inputStream)

  Updates the index to point at the provided resource, then returns itself.

• index

  public SamInputResource index(URL url)

  Updates the index to point at the provided resource, then returns itself.

• index

  public SamInputResource index(SeekableStream seekableStream)

  Updates the index to point at the provided resource, then returns itself.