htsjdk.samtools

Class Cigar

java.lang.Object

htsjdk.samtools.Cigar

All Implemented Interfaces:

java.io.Serializable

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

A list of CigarElements, which describes how a read aligns with the reference. E.g. the Cigar string 10M1D25M means * match or mismatch for 10 bases * deletion of 1 base * match or mismatch for 25 bases c.f. http://samtools.sourceforge.net/SAM1.pdf for complete CIGAR specification.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static long	serialVersionUID

Constructor Summary

Constructors

Constructor and Description
Cigar()
Cigar(java.util.List<CigarElement> cigarElements)

Method Summary

Methods

Modifier and Type	Method and Description
void	add(CigarElement cigarElement)
boolean	equals(java.lang.Object o)
CigarElement	getCigarElement(int i)
java.util.List<CigarElement>	getCigarElements()
int	getPaddedReferenceLength()
int	getReadLength()
static int	getReadLength(java.util.List<CigarElement> cigarElements)
int	getReferenceLength()
int	hashCode()
boolean	isEmpty()
java.util.List<SAMValidationError>	isValid(java.lang.String readName, long recordNumber) Exhaustive validation of CIGAR.
int	numCigarElements()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

Cigar

public Cigar()

Cigar

public Cigar(java.util.List<CigarElement> cigarElements)

Method Detail

getCigarElements

public java.util.List<CigarElement> getCigarElements()

getCigarElement

public CigarElement getCigarElement(int i)

add

public void add(CigarElement cigarElement)

numCigarElements

public int numCigarElements()

isEmpty

public boolean isEmpty()

getReferenceLength

public int getReferenceLength()

Returns:

The number of reference bases that the read covers, excluding padding.

getPaddedReferenceLength

public int getPaddedReferenceLength()

Returns:

The number of reference bases that the read covers, including padding.

getReadLength

public int getReadLength()

Returns:

The number of read bases that the read covers.

getReadLength

public static int getReadLength(java.util.List<CigarElement> cigarElements)

Returns:

The number of read bases that the read covers.

isValid

public java.util.List<SAMValidationError> isValid(java.lang.String readName,
                                         long recordNumber)

Exhaustive validation of CIGAR. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable.

Parameters:

readName - For error reporting only. May be null if not known.

recordNumber - For error reporting only. May be -1 if not known.

Returns:

List of validation errors, or null if no errors.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object