LinearIndex (htsjdk 2.23.0 API)

java.lang.Object
- htsjdk.samtools.LinearIndex

```
public class LinearIndex
extends Object
```
The linear index associated with a given reference in a BAM index.

Field Summary

Fields
Modifier and Type Field Description

static int BAM_LIDX_SHIFT

static int MAX_LINEAR_INDEX_SIZE

Constructor Summary

Constructors
Constructor Description

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static int`	`convertToLinearIndexOffset(int contigPos)`
`boolean`	`equals(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(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object