Package htsjdk.samtools.util

Class SamRecordIntervalIteratorFactory

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	Description
SamRecordIntervalIteratorFactory()

Method Summary

Modifier and Type	Method	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 Details

SamRecordIntervalIteratorFactory

public SamRecordIntervalIteratorFactory()

Method Details

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.