Package htsjdk.samtools.sra
Class SRAAlignmentIterator
- java.lang.Object
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- htsjdk.samtools.sra.SRAAlignmentIterator
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- All Implemented Interfaces:
CloseableIterator<SAMRecord>
,Closeable
,AutoCloseable
,Iterator<SAMRecord>
public class SRAAlignmentIterator extends Object implements CloseableIterator<SAMRecord>
Iterator for aligned reads. Is used from SRAIterator. Created by andrii.nikitiuk on 9/3/15.
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Constructor Summary
Constructors Constructor Description SRAAlignmentIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Should be implemented to close/release any underlying resources.boolean
hasNext()
SAMRecord
next()
void
remove()
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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SRAAlignmentIterator
public SRAAlignmentIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk)
- Parameters:
run
- opened read collectionheader
- sam headercachedReferences
- list of cached references shared among all iterators from a single SRAFileReaderrecordRangeInfo
- info about record ranges withing SRA archivechunk
- used to determine which alignments the iterator should return
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Method Detail
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setValidationStringency
public void setValidationStringency(ValidationStringency validationStringency)
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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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