htsjdk.samtools

Class SAMFileSource

java.lang.Object

htsjdk.samtools.SAMFileSource

public class SAMFileSource
extends java.lang.Object

Represents the origin of a SAM record.

Constructor Summary

Constructors

Constructor and Description
SAMFileSource(SamReader reader, SAMFileSpan filePointer) Create a new SAMFileSource with the given reader and file pointer.

Method Summary

Methods

Modifier and Type	Method and Description
SAMFileSpan	getFilePointer() A pointer to the region on disk from which the read originated.
SamReader	getReader() Retrieves the reader from which this read was initially retrieved.

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMFileSource

public SAMFileSource(SamReader reader,
             SAMFileSpan filePointer)

Create a new SAMFileSource with the given reader and file pointer.

Parameters:

reader - reader.

filePointer - File pointer.

Method Detail

getReader

public SamReader getReader()

Retrieves the reader from which this read was initially retrieved.

Returns:

The reader.

getFilePointer

public SAMFileSpan getFilePointer()

A pointer to the region on disk from which the read originated.

Returns:

A pointer within the file.