Package htsjdk.samtools
Class SamReader.AssertingIterator
- java.lang.Object
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- htsjdk.samtools.SamReader.AssertingIterator
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- All Implemented Interfaces:
SAMRecordIterator
,CloseableIterator<SAMRecord>
,Closeable
,AutoCloseable
,Iterator<SAMRecord>
- Enclosing interface:
- SamReader
public static class SamReader.AssertingIterator extends Object implements SAMRecordIterator
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Constructor Summary
Constructors Constructor Description AssertingIterator(CloseableIterator<SAMRecord> iterator)
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Method Summary
All Methods Instance Methods Concrete Methods 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.void
close()
Should be implemented to close/release any underlying resources.boolean
hasNext()
SAMRecord
next()
void
remove()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Detail
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AssertingIterator
public AssertingIterator(CloseableIterator<SAMRecord> iterator)
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Method Detail
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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 interfaceSAMRecordIterator
- Parameters:
sortOrder
- The order in which records are expected to be returned- Returns:
- This SAMRecordIterator
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close
public void close()
Description copied from interface:CloseableIterator
Should be implemented to close/release any underlying resources.- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfaceCloseableIterator<SAMRecord>
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