Package htsjdk.samtools.reference

Class ReferenceSequence

java.lang.Object

htsjdk.samtools.reference.ReferenceSequence

All Implemented Interfaces:

HtsRecord

public class ReferenceSequence
extends Object
implements HtsRecord

Wrapper around a reference sequence that has been read from a reference file.

Constructor Summary

Constructors

Constructor	Description
ReferenceSequence(String name, int index, byte[] bases)	creates a fully formed ReferenceSequence

Method Summary

Modifier and Type	Method	Description
byte[]	getBases()	Gets the array of bases that define this sequence.
String	getBaseString()	Returns the bases represented by this ReferenceSequence as a String.
int	getContigIndex()	Gets the 0-based index of this contig in the source file from which it came.
String	getName()	Gets the set of names given to this sequence in the source file.
int	length()	Gets the length of this reference sequence in bases.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

ReferenceSequence

public ReferenceSequence(String name,
 int index,
 byte[] bases)

creates a fully formed ReferenceSequence

Parameters:

name - the name of the sequence from the source file

index - the zero based index of this contig in the source file

bases - the bases themselves stored as one-byte characters

Method Details

getName

public String getName()

Gets the set of names given to this sequence in the source file.

getBases

public byte[] getBases()

Gets the array of bases that define this sequence. The bases can include any letter and possibly include masking information in the form of lower case letters. This array is mutable (obviously!) and it NOT a clone of the array held interally. Do not modify it!!!

getBaseString

public String getBaseString()

Returns the bases represented by this ReferenceSequence as a String. Since this will copy the bases and convert them to two-byte characters, this should not be used on very long reference sequences, but as a convenience when manipulating short sequences returned by ReferenceSequenceFile.getSubsequenceAt(String, long, long)

Returns:

The set of bases represented by this ReferenceSequence, as a String

getContigIndex

public int getContigIndex()

Gets the 0-based index of this contig in the source file from which it came.

length

public int length()

Gets the length of this reference sequence in bases.

toString

public String toString()

Overrides:

toString in class Object