public class SamRecordIntervalIteratorFactory
extends java.lang.Object
SamReader that only returns reads that overlap one of the intervals
in an interval list.| Constructor and Description |
|---|
SamRecordIntervalIteratorFactory() |
| Modifier and Type | Method and Description |
|---|---|
CloseableIterator<SAMRecord> |
makeSamRecordIntervalIterator(SamReader samReader,
java.util.List<Interval> uniqueIntervals,
boolean useIndex) |
public CloseableIterator<SAMRecord> makeSamRecordIntervalIterator(SamReader samReader, java.util.List<Interval> uniqueIntervals, boolean useIndex)
samReader - uniqueIntervals - list of intervals of interest, with overlaps merged, in coordinate orderuseIndex - if false, do not use a BAM index even if it is present.