IntervalListReferenceSequenceMask (htsjdk 2.14.3 API)

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java.lang.Object
- htsjdk.samtools.util.IntervalListReferenceSequenceMask

All Implemented Interfaces:

ReferenceSequenceMask
```
public class IntervalListReferenceSequenceMask
extends Object
implements ReferenceSequenceMask
```
Serve up loci of interest based on an interval list.

Constructor Summary

Constructors
Constructor Description

IntervalListReferenceSequenceMask(IntervalList intervalList)

Method Summary

All Methods Instance Methods Concrete 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.
`SAMFileHeader`	`getHeader()`
`int`	`getMaxPosition()`
`int`	`getMaxSequenceIndex()`
`int`	`nextPosition(int sequenceIndex, int position)`	It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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