Package htsjdk.samtools
Class CRAMIterator
- java.lang.Object
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- htsjdk.samtools.CRAMIterator
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- All Implemented Interfaces:
SAMRecordIterator
,CloseableIterator<SAMRecord>
,Closeable
,AutoCloseable
,Iterator<SAMRecord>
public class CRAMIterator extends Object implements SAMRecordIterator, Closeable
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Constructor Summary
Constructors Constructor Description CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency, QueryInterval[] queryIntervals, long[] coordinates)
CRAMIterator(InputStream inputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
advanceToAlignmentInContainer(int refIndex, int pos)
Skip cached records until given alignment start position.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.CramHeader
getCramHeader()
SamReader
getFileSource()
long
getFirstContainerOffset()
SAMFileHeader
getSAMFileHeader()
ValidationStringency
getValidationStringency()
boolean
hasNext()
SAMRecord
next()
void
remove()
void
setFileSource(SamReader mReader)
void
setValidationStringency(ValidationStringency validationStringency)
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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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CRAMIterator
public CRAMIterator(InputStream inputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)
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CRAMIterator
public CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency, QueryInterval[] queryIntervals, long[] coordinates)
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Method Detail
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advanceToAlignmentInContainer
public boolean advanceToAlignmentInContainer(int refIndex, int pos)
Skip cached records until given alignment start position.- Parameters:
refIndex
- reference sequence indexpos
- alignment start to skip to
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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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getFirstContainerOffset
public long getFirstContainerOffset()
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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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getCramHeader
public CramHeader getCramHeader()
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getValidationStringency
public ValidationStringency getValidationStringency()
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setValidationStringency
public void setValidationStringency(ValidationStringency validationStringency)
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getFileSource
public SamReader getFileSource()
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setFileSource
public void setFileSource(SamReader mReader)
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getSAMFileHeader
public SAMFileHeader getSAMFileHeader()
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