SamInputResource (htsjdk 3.0.5 API)

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

All Methods Static Methods Instance Methods Concrete 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(java.nio.file.Path path)` Updates the index to point at the provided resource, then returns itself.
`SamInputResource`	`index(java.nio.file.Path path, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper)` Updates the index to point at the provided resource, with the provided wrapper, 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(java.nio.file.Path path)` Creates a `SamInputResource` reading from the provided resource, with no index.
`static SamInputResource`	`of(java.nio.file.Path path, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.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.
`static SamInputResource`	`of(SeekableStream seekableStream)` Creates a `SamInputResource` reading from the provided resource, with no index.
`static SamInputResource`	`of(SRAAccession acc)`
`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.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(java.net.URI uri, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.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(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.nio.file.Path path)
```
    Creates a SamInputResource reading from the provided resource, with no index.
  - of
```
public static SamInputResource of(java.nio.file.Path path,
                                  java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.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(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(SRAAccession acc)
```
  - of
```
public static SamInputResource of(java.net.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(java.net.URI uri,
                                  java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.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(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.nio.file.Path path)
```
    Updates the index to point at the provided resource, then returns itself.
  - index
```
public SamInputResource index(java.nio.file.Path path,
                              java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper)
```
    Updates the index to point at the provided resource, with the provided wrapper, 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.

Class SamInputResource

Method Summary

Methods inherited from class java.lang.Object

Method Detail

toString

of

of

of

of

of

of

of

of

of

of

index

index

index

index

index

index