SamRecordIntervalIteratorFactory (htsjdk 2.8.1 API)

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

```
public class SamRecordIntervalIteratorFactory
extends Object
```
Create an iterator over a SamReader that only returns reads that overlap one of the intervals in an interval list.

Constructor Summary

Constructors
Constructor and Description

SamRecordIntervalIteratorFactory()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`CloseableIterator<SAMRecord>`	`makeSamRecordIntervalIterator(SamReader samReader, List<Interval> uniqueIntervals, boolean useIndex)`

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

- Constructor Detail
  - SamRecordIntervalIteratorFactory
```
public SamRecordIntervalIteratorFactory()
```
- Method Detail
  - makeSamRecordIntervalIterator
```
public CloseableIterator<SAMRecord> makeSamRecordIntervalIterator(SamReader samReader,
                                                                  List<Interval> uniqueIntervals,
                                                                  boolean useIndex)
```
    Parameters:
    
    samReader -
    
    uniqueIntervals - list of intervals of interest, with overlaps merged, in coordinate order
    
    useIndex - if false, do not use a BAM index even if it is present.
    
    Returns:
    
    an iterator that will be filtered so that only SAMRecords overlapping the intervals in uniqueIntervals will be returned. If a BAM index is available, it will be used to improve performance. Note however that if there are many intervals that cover a great deal of the genome, using the BAM index may actually make performance worse.

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