htsjdk.samtools

Class SBIIndexMerger

java.lang.Object

htsjdk.samtools.IndexMerger<SBIIndex>

htsjdk.samtools.SBIIndexMerger

public final class SBIIndexMerger
extends IndexMerger<SBIIndex>

Merges SBI files for parts of a file that have been concatenated.

Field Summary

Fields inherited from class htsjdk.samtools.IndexMerger

out, partLengths

Constructor Summary

Constructors

Constructor and Description
SBIIndexMerger(java.io.OutputStream out, long headerLength) Prepare to merge SBI indexes.

Method Summary

Modifier and Type	Method and Description
void	finish(long dataFileLength) Complete the index, and close the output stream.
void	processIndex(SBIIndex index, long partLength) Add an index for a part of the data file to the merged index.

Methods inherited from class java.lang.Object

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

Constructor Detail

SBIIndexMerger

public SBIIndexMerger(java.io.OutputStream out,
                      long headerLength)

Prepare to merge SBI indexes.

Parameters:

out - the stream to write the merged index to

headerLength - the length of any header that precedes the first part of the data file with an index

Method Detail

processIndex

public void processIndex(SBIIndex index,
                         long partLength)

Add an index for a part of the data file to the merged index. This method should be called for each index for the data file parts, in order.

Specified by:

processIndex in class IndexMerger<SBIIndex>

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)

Complete the index, and close the output stream.

Specified by:

finish in class IndexMerger<SBIIndex>

Parameters:

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