htsjdk.samtools.util

Class SamRecordIntervalIteratorFactory

java.lang.Object

htsjdk.samtools.util.SamRecordIntervalIteratorFactory

public class SamRecordIntervalIteratorFactory
extends java.lang.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

Modifier and Type	Method and Description
CloseableIterator<SAMRecord>	makeSamRecordIntervalIterator(SamReader samReader, java.util.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,
                                                                  java.util.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.