/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import htsjdk.samtools.util.CloseableIterator;
/**
* A general interface that adds functionality to a CloseableIterator of
* SAMRecords. Currently, this interface is implemented by iterators that
* want to validate as they are iterating that that the records in the
* underlying SAM/BAM file are in a particular order.
*/
public interface SAMRecordIterator extends CloseableIterator<SAMRecord> {
/**
* 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.
*
* @param sortOrder The order in which records are expected to be returned
* @return This SAMRecordIterator
*/
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder);
}