htsjdk.samtools

Class SamInputResource

java.lang.Object

htsjdk.samtools.SamInputResource

public class SamInputResource
extends java.lang.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

Methods

Modifier and Type	Method and Description
SamInputResource	index(java.io.File file) Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(java.io.InputStream inputStream) Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(SeekableStream seekableStream) Updates the index to point at the provided resource, then returns itself.
SamInputResource	index(java.net.URL url) Updates the index to point at the provided resource, then returns itself.
static SamInputResource	of(java.io.File file) Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(java.io.InputStream inputStream) Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(SeekableStream seekableStream) Creates a SamInputResource reading from the provided resource, with no index.
static SamInputResource	of(java.lang.String string) Creates a SamInputResource from a string specifying *either* a url or a file path
static SamInputResource	of(java.net.URL url) Creates a SamInputResource reading from the provided resource, with no index.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

of

public static SamInputResource of(java.io.File file)

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

of

public static SamInputResource of(java.io.InputStream inputStream)

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

of

public static SamInputResource of(java.net.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(java.lang.String string)

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

index

public SamInputResource index(java.io.File file)

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

index

public SamInputResource index(java.io.InputStream inputStream)

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

index

public SamInputResource index(java.net.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.