htsjdk.samtools

Class SBIIndex

java.lang.Object

htsjdk.samtools.SBIIndex

All Implemented Interfaces:

java.io.Serializable

public final class SBIIndex
extends java.lang.Object
implements java.io.Serializable

SBI is an index into BGZF-compressed data files, which has an entry for the file position of the start of every nth record. Reads files that were created by BAMSBIIndexer.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SBIIndex.Header

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	FILE_EXTENSION Deprecated. since June 2019 Use FileExtensions.SBI instead.

Constructor Summary

Constructors

Constructor and Description
SBIIndex(SBIIndex.Header header, long[] virtualOffsets) Create an in-memory SBI with the given virtual offsets.

Method Summary

Modifier and Type	Method and Description
long	dataFileLength() Returns the length of the data file in bytes.
boolean	equals(java.lang.Object o)
Chunk	getChunk(long splitStart, long splitEnd) Return a chunk that corresponds to the given range in the data file.
long	getGranularity() Returns the granularity of the index, that is the number of alignments between subsequent entries in the index, or zero if not specified.
SBIIndex.Header	getHeader() Returns the index header.
long[]	getVirtualOffsets() Returns the entries in the index.
int	hashCode()
static SBIIndex	load(java.io.InputStream in) Load an SBI into memory from a stream.
static SBIIndex	load(java.nio.file.Path path) Load an SBI into memory from a path.
long	size() Returns number of entries in the index.
java.util.List<Chunk>	split(long splitSize) Split the data file for this index into non-overlapping chunks of roughly the given size that cover the whole file and that can be read independently of one another.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

FILE_EXTENSION

@Deprecated
public static final java.lang.String FILE_EXTENSION

Deprecated. since June 2019 Use FileExtensions.SBI instead.

See Also:

Constant Field Values

Constructor Detail

SBIIndex

public SBIIndex(SBIIndex.Header header,
                long[] virtualOffsets)

Create an in-memory SBI with the given virtual offsets.

Parameters:

virtualOffsets - the offsets in the index

Method Detail

load

public static SBIIndex load(java.nio.file.Path path)
                     throws java.io.IOException

Load an SBI into memory from a path.

Parameters:

path - the path to the SBI file

Throws:

java.io.IOException - as per java IO contract

load

public static SBIIndex load(java.io.InputStream in)

Load an SBI into memory from a stream.

Parameters:

in - the stream to read the SBI from

getHeader

public SBIIndex.Header getHeader()

Returns the index header.

Returns:

the header

getGranularity

public long getGranularity()

Returns the granularity of the index, that is the number of alignments between subsequent entries in the index, or zero if not specified.

Returns:

the granularity of the index

getVirtualOffsets

public long[] getVirtualOffsets()

Returns the entries in the index.

Returns:

an array of file pointers for all the alignment offsets in the index, in ascending order. The last virtual file pointer is the position at which the next record would start if it were added to the file.

size

public long size()

Returns number of entries in the index.

Returns:

the number of virtual offsets in the index

dataFileLength

public long dataFileLength()

Returns the length of the data file in bytes.

Returns:

the length of the data file in bytes

split

public java.util.List<Chunk> split(long splitSize)

Split the data file for this index into non-overlapping chunks of roughly the given size that cover the whole file and that can be read independently of one another.

Parameters:

splitSize - the rough size of each split in bytes

Returns:

a list of contiguous, non-overlapping, sorted chunks that cover the whole data file

See Also:

getChunk(long, long)

getChunk

public Chunk getChunk(long splitStart,
                      long splitEnd)

Return a chunk that corresponds to the given range in the data file. Note that the chunk does not necessarily completely cover the given range, however this method will map a set of contiguous, non-overlapping file ranges that cover the whole data file to a set of contiguous, non-overlapping chunks that cover the whole data file.

Parameters:

splitStart - the start of the file range (inclusive)

splitEnd - the start of the file range (exclusive)

Returns:

a chunk whose virtual start is at the first alignment start position that is greater than or equal to the given split start position, and whose virtual end is at the first alignment start position that is greater than or equal to the given split end position, or null if the chunk would be empty.

See Also:

split(long)

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object