ReferenceSequenceMask (htsjdk 2.24.1 API)

All Known Implementing Classes:

IntervalListReferenceSequenceMask, WholeGenomeReferenceSequenceMask
```
public interface ReferenceSequenceMask
```
Interface for specifying loci of interest for genotype calling and other operations. It is a requirement that the sequences be probed in ascending order.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`boolean`	`get(int sequenceIndex, int position)`	It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
`int`	`getMaxPosition()`
`int`	`getMaxSequenceIndex()`
`int`	`nextPosition(int sequenceIndex, int position)`	It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

- Method Detail
  - get
```
boolean get(int sequenceIndex,
            int position)
```
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    
    Returns:
    
    true if the mask is set for the given sequence and position
  - nextPosition
```
int nextPosition(int sequenceIndex,
                 int position)
```
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    
    Returns:
    
    the next pos on the given sequence >= position that is set, or -1 if there are no more set positions
  - getMaxSequenceIndex
```
int getMaxSequenceIndex()
```
    Returns:
    
    Largest sequence index for which there are set bits.
  - getMaxPosition
```
int getMaxPosition()
```
    Returns:
    
    the largest position on the last sequence index