Package htsjdk.samtools

Interface SAMRecordIterator

All Superinterfaces:

AutoCloseable, Closeable, CloseableIterator<SAMRecord>, Iterator<SAMRecord>

All Known Implementing Classes:

CRAMIterator, SamReader.AssertingIterator, SRAIterator

public interface SAMRecordIterator
extends CloseableIterator<SAMRecord>

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 the records in the underlying SAM/BAM file are in a particular order.

Method Summary

Modifier and Type	Method	Description
SAMRecordIterator	assertSorted(SAMFileHeader.SortOrder sortOrder)	Establishes that records returned by this iterator are expected to be in the specified sort order.

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

close, stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next, remove

Method Details

assertSorted

SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)

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.

Parameters:

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

Returns:

This SAMRecordIterator