htsjdk.samtools

Class LinearIndex

java.lang.Object

htsjdk.samtools.LinearIndex

public class LinearIndex
extends java.lang.Object

The linear index associated with a given reference in a BAM index.

Field Summary

Fields

Modifier and Type	Field and Description
static int	BAM_LIDX_SHIFT
static int	MAX_LINEAR_INDEX_SIZE

Constructor Summary

Constructors

Constructor and Description
LinearIndex(int referenceSequence, int indexStart, long[] indexEntries)

Method Summary

Modifier and Type	Method and Description
static int	convertToLinearIndexOffset(int contigPos)
boolean	equals(java.lang.Object o)
long	get(int index)
long[]	getIndexEntries() Direct access to the array.
int	getIndexStart()
long	getMinimumOffset(int startPos) Gets the minimum offset of any alignment start appearing in this index, according to the linear index.
int	getReferenceSequence()
int	hashCode()
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

MAX_LINEAR_INDEX_SIZE

public static final int MAX_LINEAR_INDEX_SIZE

BAM_LIDX_SHIFT

public static final int BAM_LIDX_SHIFT

See Also:

Constant Field Values

Constructor Detail

LinearIndex

public LinearIndex(int referenceSequence,
                   int indexStart,
                   long[] indexEntries)

Method Detail

getReferenceSequence

public int getReferenceSequence()

size

public int size()

get

public long get(int index)

convertToLinearIndexOffset

public static int convertToLinearIndexOffset(int contigPos)

getMinimumOffset

public long getMinimumOffset(int startPos)

Gets the minimum offset of any alignment start appearing in this index, according to the linear index.

Parameters:

startPos - Starting position for this query.

Returns:

The minimum offset, in chunk format, of any read appearing in this position.

getIndexEntries

public long[] getIndexEntries()

Direct access to the array. Be careful!

Returns:

The elements of the linear index.

getIndexStart

public int getIndexStart()

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