public class LinearIndex
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
BAM_LIDX_SHIFT |
static int |
MAX_LINEAR_INDEX_SIZE |
Constructor and Description |
---|
LinearIndex(int referenceSequence,
int indexStart,
long[] indexEntries) |
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() |
public static final int MAX_LINEAR_INDEX_SIZE
public static final int BAM_LIDX_SHIFT
public LinearIndex(int referenceSequence, int indexStart, long[] indexEntries)
public int getReferenceSequence()
public int size()
public long get(int index)
public static int convertToLinearIndexOffset(int contigPos)
public long getMinimumOffset(int startPos)
startPos
- Starting position for this query.public long[] getIndexEntries()
public int getIndexStart()
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object