htsjdk.samtools.cram.ref

Class ReferenceContext

java.lang.Object

htsjdk.samtools.cram.ref.ReferenceContext

All Implemented Interfaces:

java.lang.Comparable<ReferenceContext>

public class ReferenceContext
extends java.lang.Object
implements java.lang.Comparable<ReferenceContext>

Represents the current state of reference sequence processing. Are we handling MULTIPLE_REFERENCE_TYPE records (-2, from the CRAM spec)? Are we handling UNMAPPED_UNPLACED_TYPE records (-1, from the CRAM spec)? Or are we handing a known SINGLE_REFERENCE_TYPE sequence (0 or higher, from the CRAM spec))?

Field Summary

Fields

Modifier and Type	Field and Description
static ReferenceContext	MULTIPLE_REFERENCE_CONTEXT
static int	MULTIPLE_REFERENCE_ID
static ReferenceContext	UNMAPPED_UNPLACED_CONTEXT
static int	UNMAPPED_UNPLACED_ID

Constructor Summary

Constructors

Constructor and Description
ReferenceContext(int serializableSequenceId) Create a ReferenceContext from a serializable sequence ID 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference

Method Summary

Modifier and Type	Method and Description
int	compareTo(ReferenceContext o)
boolean	equals(java.lang.Object o)
int	getSequenceId() Get the valid sequence ID, if single-reference
int	getSerializableId() Get the ReferenceContext sequence ID or sentinel value, suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference
ReferenceContextType	getType() Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE
int	hashCode()
boolean	isMappedSingleRef() Does this ReferenceContext refer to reads placed on a single reference (whether their unmapped flags are set or not)?
boolean	isMultiRef() Does this ReferenceContext refer to: - reads placed on multiple references - or a combination of placed and unplaced reads?
boolean	isUnmappedUnplaced() Does this ReferenceContext refer to only unmapped-unplaced reads? Note: not a guarantee that the unmapped flag is set for all records
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

MULTIPLE_REFERENCE_ID

public static final int MULTIPLE_REFERENCE_ID

See Also:

Constant Field Values

UNMAPPED_UNPLACED_ID

public static final int UNMAPPED_UNPLACED_ID

See Also:

Constant Field Values

MULTIPLE_REFERENCE_CONTEXT

public static final ReferenceContext MULTIPLE_REFERENCE_CONTEXT

UNMAPPED_UNPLACED_CONTEXT

public static final ReferenceContext UNMAPPED_UNPLACED_CONTEXT

Constructor Detail

ReferenceContext

public ReferenceContext(int serializableSequenceId)

Create a ReferenceContext from a serializable sequence ID 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference

Parameters:

serializableSequenceId - the sequence ID or sentinel value for constructing this ReferenceContext

Method Detail

getType

public ReferenceContextType getType()

Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE

Returns:

the ReferenceContextType enum

getSerializableId

public int getSerializableId()

Get the ReferenceContext sequence ID or sentinel value, suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference

Returns:

the sequence ID

getSequenceId

public int getSequenceId()

Get the valid sequence ID, if single-reference

Returns:

the sequence ID

Throws:

CRAMException - if this is not single-ref

isUnmappedUnplaced

public boolean isUnmappedUnplaced()

Does this ReferenceContext refer to only unmapped-unplaced reads? Note: not a guarantee that the unmapped flag is set for all records

Returns:

true if the ReferenceContext refers only to unmapped-unplaced reads

See Also:

CramCompressionRecord.isPlaced()

isMultiRef

public boolean isMultiRef()

Does this ReferenceContext refer to: - reads placed on multiple references - or a combination of placed and unplaced reads?

Returns:

true if the ReferenceContext relates to reads placed on multiple references or a combination of placed and unplaced reads

isMappedSingleRef

public boolean isMappedSingleRef()

Does this ReferenceContext refer to reads placed on a single reference (whether their unmapped flags are set or not)?

Returns:

true if all reads referred to by this ReferenceContext are placed on a single reference

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

compareTo

public int compareTo(ReferenceContext o)

Specified by:

compareTo in interface java.lang.Comparable<ReferenceContext>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object