Package htsjdk.samtools.cram

Class CRAIIndex

java.lang.Object

htsjdk.samtools.cram.CRAIIndex

public class CRAIIndex
extends Object

CRAI index used for CRAM files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CRAI_INDEX_SUFFIX	Deprecated. since June 2019 Use FileExtensions.CRAM_INDEX instead.

Constructor Summary

Constructors

Constructor	Description
CRAIIndex()

Method Summary

Modifier and Type	Method	Description
void	addEntries(Collection<CRAIEntry> toAdd)	Add multiple entries to the CRAI index.
void	addEntry(CRAIEntry entry)	Add a single entry to the CRAI index.
static List<CRAIEntry>	find(List<CRAIEntry> list, int seqId, int start, int span)	Currently unused, but retained for the native rai query implementation
static int	findLastAlignedEntry(List<CRAIEntry> list)	Currently unused, but retained for the native rai query implementation
List<CRAIEntry>	getCRAIEntries()
static CRAIEntry	getLeftmost(List<CRAIEntry> list)	Currently unused, but retained for the native rai query implementation
static SeekableStream	openCraiFileAsBaiStream(File cramIndexFile, SAMSequenceDictionary dictionary)
static SeekableStream	openCraiFileAsBaiStream(InputStream indexStream, SAMSequenceDictionary dictionary)
void	processContainer(Container container)	Create index entries for a single container.
void	writeIndex(OutputStream os)	Write out the index to an output stream;

Methods inherited from class java.lang.Object

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

Field Details

CRAI_INDEX_SUFFIX

@Deprecated
public static final String CRAI_INDEX_SUFFIX

Deprecated.

since June 2019 Use FileExtensions.CRAM_INDEX instead.

See Also:

• Constant Field Values

Constructor Details

CRAIIndex

public CRAIIndex()

Method Details

addEntry

public void addEntry(CRAIEntry entry)

Add a single entry to the CRAI index.

Parameters:

entry - entry to be added

addEntries

public void addEntries(Collection<CRAIEntry> toAdd)

Add multiple entries to the CRAI index.

Parameters:

toAdd - entries to be added

getCRAIEntries

public List<CRAIEntry> getCRAIEntries()

writeIndex

public void writeIndex(OutputStream os)

Write out the index to an output stream;

Parameters:

os - Stream to write index to

processContainer

public void processContainer(Container container)

Create index entries for a single container.

Parameters:

container - the container to index

openCraiFileAsBaiStream

public static SeekableStream openCraiFileAsBaiStream(File cramIndexFile,
 SAMSequenceDictionary dictionary)

openCraiFileAsBaiStream

public static SeekableStream openCraiFileAsBaiStream(InputStream indexStream,
 SAMSequenceDictionary dictionary)

find

public static List<CRAIEntry> find(List<CRAIEntry> list,
 int seqId,
 int start,
 int span)

Currently unused, but retained for the native rai query implementation

getLeftmost

public static CRAIEntry getLeftmost(List<CRAIEntry> list)

Currently unused, but retained for the native rai query implementation

findLastAlignedEntry

public static int findLastAlignedEntry(List<CRAIEntry> list)

Currently unused, but retained for the native rai query implementation