htsjdk.samtools.cram

Class CRAIIndexMerger

java.lang.Object

htsjdk.samtools.IndexMerger<CRAIIndex>

htsjdk.samtools.cram.CRAIIndexMerger

public final class CRAIIndexMerger
extends IndexMerger<CRAIIndex>

Merges CRAM index files for (headerless) parts of a CRAM file into a single index file. A partitioned CRAM is a directory containing the following files:

1. A file named header containing all header bytes (CRAM header and CRAM container containing the BAM header).
2. Zero or more files named part-00000, part-00001, ... etc, containing CRAM containers.
3. A file named terminator containing a CRAM end-of-file marker container.

If an index is required, a CRAM index can be generated for each (headerless) part file. These files should be named .part-00000.crai, .part-00001.crai, ... etc. Note the leading . to make the files hidden. This format has the following properties:

• Parts and their indexes may be written in parallel, since one part file can be written independently of the others.
• A CRAM file can be created from a partitioned CRAM file by merging all the non-hidden files (header, part-00000, part-00001, ..., terminator).
• A CRAM index can be created from a partitioned CRAM file by merging all of the hidden files with a .crai suffix. Note that this is not a simple file concatenation operation. See CRAIIndexMerger.

Field Summary

Fields inherited from class htsjdk.samtools.IndexMerger

out, partLengths

Constructor Summary

Constructors

Constructor and Description
CRAIIndexMerger(java.io.OutputStream out, long headerLength)

Method Summary

Modifier and Type	Method and Description
void	finish(long dataFileLength) Finish merging the indexes, and close the output stream.
void	processIndex(CRAIIndex index, long partLength) Process the next index and add to the merged index.

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAIIndexMerger

public CRAIIndexMerger(java.io.OutputStream out,
                       long headerLength)
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

processIndex

public void processIndex(CRAIIndex index,
                         long partLength)

Description copied from class: IndexMerger

Process the next index and add to the merged index.

Specified by:

processIndex in class IndexMerger<CRAIIndex>

Parameters:

index - the index to merge

partLength - the length of the part file corresponding to the index, in bytes.

finish

public void finish(long dataFileLength)
            throws java.io.IOException

Description copied from class: IndexMerger

Finish merging the indexes, and close the output stream.

Specified by:

finish in class IndexMerger<CRAIIndex>

Parameters:

dataFileLength - the length of the total data file, in bytes.

Throws:

java.io.IOException - if an error occurs