htsjdk.samtools

Class CRAMFileReader.IntervalIterator

java.lang.Object

htsjdk.samtools.CRAMFileReader.IntervalIterator

All Implemented Interfaces:

SAMRecordIterator, CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

Enclosing class:

CRAMFileReader

public static class CRAMFileReader.IntervalIterator
extends java.lang.Object
implements SAMRecordIterator

Constructor Summary

Constructors

Constructor and Description
IntervalIterator(CloseableIterator<SAMRecord> delegate, QueryInterval interval)
IntervalIterator(CloseableIterator<SAMRecord> delegate, QueryInterval interval, boolean overlap)

Method Summary

Modifier and Type	Method and Description
SAMRecordIterator	assertSorted(SAMFileHeader.SortOrder sortOrder) Establishes that records returned by this iterator are expected to be in the specified sort order.
void	close() Should be implemented to close/release any underlying resources.
boolean	hasNext()
SAMRecord	next()
void	remove()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

IntervalIterator

public IntervalIterator(CloseableIterator<SAMRecord> delegate,
                        QueryInterval interval)

IntervalIterator

public IntervalIterator(CloseableIterator<SAMRecord> delegate,
                        QueryInterval interval,
                        boolean overlap)

Method Detail

assertSorted

public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)

Description copied from interface: SAMRecordIterator

Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.

Specified by:

assertSorted in interface SAMRecordIterator

Parameters:

sortOrder - The order in which records are expected to be returned

Returns:

This SAMRecordIterator

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Specified by:

next in interface java.util.Iterator<SAMRecord>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<SAMRecord>