Package htsjdk.samtools

Class SamInputResource

java.lang.Object

htsjdk.samtools.SamInputResource

public class SamInputResource
extends Object

Describes a SAM-like resource, including its data (where the records are), and optionally an index.

A data or index source may originate from a File, InputStream, URL, or SeekableStream; look for the appropriate overload for htsjdk.samtools.SamInputResource#of().

Method Summary

Modifier and Type	Method	Description
SamInputResource	index(SeekableStream seekableStream)	Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(File file)	Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(InputStream inputStream)	Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(URL url)	Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(Path path)	Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(Path path, Function<SeekableByteChannel,SeekableByteChannel> wrapper)	Updates the index to point at the provided resource, with the provided wrapper, then returns itself.
static SamInputResource	of(SeekableStream seekableStream)	Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(SRAAccession acc)
static SamInputResource	of(File file)	Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(InputStream inputStream)	Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(String string)	Creates a SamInputResource from a string specifying *either* a url or a file path
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.
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.
static SamInputResource	of(URL url)	Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(Path path)	Creates a SamInputResource reading from the provided resource, with no index.
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.
String	toString()

Methods inherited from class java.lang.Object

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

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.