htsjdk.samtools

Class BAMSBIIndexer

java.lang.Object

htsjdk.samtools.BAMSBIIndexer

public final class BAMSBIIndexer
extends java.lang.Object

Writes SBI files for BAM files, as understood by SBIIndex.

Constructor Summary

Constructors

Constructor and Description
BAMSBIIndexer()

Method Summary

Modifier and Type	Method and Description
static void	createIndex(java.nio.file.Path bamFile, long granularity) Perform indexing on the given BAM file, at the granularity level specified.
static void	createIndex(SeekableStream in, java.io.OutputStream out, long granularity) Perform indexing on the given BAM file, at the granularity level specified.

Methods inherited from class java.lang.Object

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

Constructor Detail

BAMSBIIndexer

public BAMSBIIndexer()

Method Detail

createIndex

public static void createIndex(java.nio.file.Path bamFile,
                               long granularity)
                        throws java.io.IOException

Perform indexing on the given BAM file, at the granularity level specified.

Parameters:

bamFile - the path to the BAM file

granularity - write the offset of every n-th alignment to the index

Throws:

java.io.IOException - as per java IO contract

createIndex

public static void createIndex(SeekableStream in,
                               java.io.OutputStream out,
                               long granularity)
                        throws java.io.IOException

Perform indexing on the given BAM file, at the granularity level specified.

Parameters:

in - a seekable stream for reading the BAM file from

out - the stream to write the index to

granularity - write the offset of every n-th alignment to the index

Throws:

java.io.IOException - as per java IO contract