htsjdk.samtools

Class CRAMBAIIndexer

java.lang.Object

htsjdk.samtools.CRAMBAIIndexer

All Implemented Interfaces:

CRAMIndexer

public class CRAMBAIIndexer
extends java.lang.Object
implements CRAMIndexer

Class for both constructing BAM index content and writing it out. There are two usage patterns: 1) Building a bam index (BAI) while building the CRAM file 2) Building a bam index (BAI) from an existing CRAI file 1) is driven by CRAMContainerStreamWriter and proceeds by calling processContainer(htsjdk.samtools.cram.structure.Container, htsjdk.samtools.ValidationStringency) after each Container is built, and finish() is called at the end. 2) is driven by CRAIIndex.openCraiFileAsBaiStream(InputStream, SAMSequenceDictionary) and proceeds by processing CRAIEntry elements obtained from CRAMCRAIIndexer.readIndex(InputStream). processAsSingleReferenceSlice(Slice) is called on each CRAIEntry and finish() is called at the end. NOTE: a third pattern of building a BAI from a CRAM file is also supported by this class, but it is unused. This would be accomplished via createIndex(SeekableStream, File, Log, ValidationStringency).

Constructor Summary

Constructors

Constructor and Description
CRAMBAIIndexer(java.io.OutputStream output, SAMFileHeader fileHeader) Create a CRAM indexer that writes BAI to a stream.

Method Summary

Modifier and Type	Method and Description
static void	createIndex(SeekableStream stream, java.io.File output, Log log, ValidationStringency validationStringency) Generates a BAI index file from an input CRAM stream
void	finish() After all the slices have been processed, finish is called.
void	processAsSingleReferenceSlice(Slice slice) Record index information for a given CRAM slice that contains either unmapped-unplaced reads, reads mapped to a single reference, or a "fake" slice which represents a portion of a multi-ref slice.
void	processContainer(Container container, ValidationStringency validationStringency) Index a container, any of mapped, unmapped and multiple references are allowed.

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMBAIIndexer

public CRAMBAIIndexer(java.io.OutputStream output,
                      SAMFileHeader fileHeader)

Create a CRAM indexer that writes BAI to a stream.

Parameters:

output - Index will be written here. output will be closed when finish() method is called.

fileHeader - header for the corresponding bam file.

Method Detail

processContainer

public void processContainer(Container container,
                             ValidationStringency validationStringency)

Index a container, any of mapped, unmapped and multiple references are allowed. The only requirement is sort order by coordinate. For multiref containers the method reads the container through unpacking all reads. This is slower than single reference but should be faster than normal reading.

Specified by:

processContainer in interface CRAMIndexer

Parameters:

container - container to be indexed

validationStringency - stringency for validating records, passed to Container.getSpans(ValidationStringency)

processAsSingleReferenceSlice

public void processAsSingleReferenceSlice(Slice slice)

Record index information for a given CRAM slice that contains either unmapped-unplaced reads, reads mapped to a single reference, or a "fake" slice which represents a portion of a multi-ref slice. If this alignment starts a new reference, write out the old reference.

Parameters:

slice - The CRAM slice or "fake" sub-slice

Throws:

SAMException - if slice refers to multiple reference sequences.

finish

public void finish()

After all the slices have been processed, finish is called. Writes any final information and closes the output file.

Specified by:

finish in interface CRAMIndexer

createIndex

public static void createIndex(SeekableStream stream,
                               java.io.File output,
                               Log log,
                               ValidationStringency validationStringency)

Generates a BAI index file from an input CRAM stream

Parameters:

stream - CRAM stream to index

output - File for output index file

log - optional Log to output progress