htsjdk.samtools

Class CRAMIndexer

java.lang.Object

htsjdk.samtools.CRAMIndexer

public class CRAMIndexer
extends java.lang.Object

Class for both constructing BAM index content and writing it out. There are two usage patterns: 1) Building a bam index from an existing cram file 2) Building a bam index while building the cram file In both cases, processAlignment is called for each cram slice and finish() is called at the end.

Constructor Summary

Constructors

Constructor and Description
CRAMIndexer(java.io.File output, SAMFileHeader fileHeader) Create a CRAM indexer that writes BAI to a file.
CRAMIndexer(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	createAndWriteIndex(java.io.File input, java.io.File output, boolean textOutput) Generates a BAM index file, either textual or binary, from an input BAI file.
static void	createIndex(SeekableStream stream, java.io.File output, Log log) Generates a BAI index file from an input CRAM stream
void	finish() After all the slices have been processed, finish is called.
void	processAlignment(Slice slice) Record any index information for a given CRAM slice.

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMIndexer

public CRAMIndexer(java.io.File output,
                   SAMFileHeader fileHeader)

Create a CRAM indexer that writes BAI to a file.

Parameters:

output - binary BAM Index (.bai) file

fileHeader - header for the corresponding bam file

CRAMIndexer

public CRAMIndexer(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

processAlignment

public void processAlignment(Slice slice)

Record any index information for a given CRAM slice. If this alignment starts a new reference, write out the old reference. Requires a non-null value for rec.getFileSource().

Parameters:

slice - The CRAM slice

finish

public void finish()

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

createAndWriteIndex

public static void createAndWriteIndex(java.io.File input,
                                       java.io.File output,
                                       boolean textOutput)

Generates a BAM index file, either textual or binary, from an input BAI file. Only used for testing, but located here for visibility into CachingBAMFileIndex.

Parameters:

output - BAM Index (.bai) file (or bai.txt file when text)

textOutput - Whether to create text output or binary

createIndex

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

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

Throws:

java.io.IOException