htsjdk.samtools

Class AlignmentBlock

java.lang.Object

htsjdk.samtools.AlignmentBlock

All Implemented Interfaces:

java.io.Serializable

public class AlignmentBlock
extends java.lang.Object
implements java.io.Serializable

Represents the contiguous alignment of a subset of read bases to a reference sequence. Simply put an alignment block tells you that read bases from readStart are aligned to the reference (matching or mismatching) from referenceStart for length bases.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static long	serialVersionUID

Method Summary

Modifier and Type	Method and Description
int	getLength() The number of contiguous bases aligned to the reference.
int	getReadStart() The first, 1-based, base in the read that is aligned to the reference reference.
int	getReferenceStart() The first, 1-based, position in the reference to which the read is aligned.

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Method Detail

getReadStart

public int getReadStart()

The first, 1-based, base in the read that is aligned to the reference reference.

getReferenceStart

public int getReferenceStart()

The first, 1-based, position in the reference to which the read is aligned.

getLength

public int getLength()

The number of contiguous bases aligned to the reference.