htsjdk.samtools

Class CRAMCRAIIndexer

java.lang.Object

htsjdk.samtools.CRAMCRAIIndexer

All Implemented Interfaces:

CRAMIndexer

public class CRAMCRAIIndexer
extends java.lang.Object
implements CRAMIndexer

Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream. There are three ways to obtain an index:

• create an index for an entire CRAM stream and write it to an output stream
• create an index on-the-fly by processing one container at a time
• read an existing index from an input stream

Constructor Summary

Constructors

Constructor and Description
CRAMCRAIIndexer(java.io.OutputStream os, SAMFileHeader samHeader) Create a CRAMCRAIIndexer that writes to the given output stream.
CRAMCRAIIndexer(java.io.OutputStream os, SAMFileHeader samHeader, java.util.Collection<CRAIEntry> entries) Create a CRAMCRAIIndexer that writes to the given output stream, initialized with a Collection of CRAIEntry objects.

Method Summary

Modifier and Type	Method and Description
void	finish() Finish creating the index by writing the accumulated entries out to the stream.
void	processContainer(Container container) Create index entries for a single container.
void	processContainer(Container container, ValidationStringency validationStringency) Create index entries for a single container.
static CRAIIndex	readIndex(java.io.InputStream is) Read an input stream containing a .crai index and return a CRAIIndex object.
static void	writeIndex(SeekableStream cramStream, java.io.OutputStream craiStream) Generate and write a CRAI index to an output stream from a CRAM input stream

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMCRAIIndexer

public CRAMCRAIIndexer(java.io.OutputStream os,
                       SAMFileHeader samHeader)

Create a CRAMCRAIIndexer that writes to the given output stream.

Parameters:

os - output stream to which the index will be written

samHeader - SAMFileHeader - user to verify sort order

CRAMCRAIIndexer

public CRAMCRAIIndexer(java.io.OutputStream os,
                       SAMFileHeader samHeader,
                       java.util.Collection<CRAIEntry> entries)

Create a CRAMCRAIIndexer that writes to the given output stream, initialized with a Collection of CRAIEntry objects.

Parameters:

os - output stream to which the index will be written

samHeader - SAMFileHeader - user to verify sort order

entries - the CRAI entries to index

Method Detail

processContainer

public void processContainer(Container container)

Create index entries for a single container.

Parameters:

container - the container to index

processContainer

public void processContainer(Container container,
                             ValidationStringency validationStringency)

Description copied from interface: CRAMIndexer

Create index entries for a single container.

Specified by:

processContainer in interface CRAMIndexer

Parameters:

container - the container to index

validationStringency - stringency for validating records (used when processing multi-reference slices, since creating an index on a multi-ref slices requires actually decoding the records in order to resove the constituent reference spans}

finish

public void finish()

Finish creating the index by writing the accumulated entries out to the stream.

Specified by:

finish in interface CRAMIndexer

writeIndex

public static void writeIndex(SeekableStream cramStream,
                              java.io.OutputStream craiStream)

Generate and write a CRAI index to an output stream from a CRAM input stream

Parameters:

cramStream - CRAM stream to index; must be coordinate sorted

craiStream - stream for output index

readIndex

public static CRAIIndex readIndex(java.io.InputStream is)

Read an input stream containing a .crai index and return a CRAIIndex object.

Parameters:

is - Input stream to read

Returns:

A CRAIIndex object representing the index.