Package htsjdk.samtools.sra
Class SRAAlignmentIterator
java.lang.Object
htsjdk.samtools.sra.SRAAlignmentIterator
- All Implemented Interfaces:
CloseableIterator<SAMRecord>
,Closeable
,AutoCloseable
,Iterator<SAMRecord>
Iterator for aligned reads.
Is used from SRAIterator.
Created by andrii.nikitiuk on 9/3/15.
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Constructor Summary
ConstructorDescriptionSRAAlignmentIterator
(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk) -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Should be implemented to close/release any underlying resources.boolean
hasNext()
next()
void
remove()
void
setValidationStringency
(ValidationStringency validationStringency) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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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 Details
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hasNext
public boolean hasNext() -
next
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remove
public void remove() -
setValidationStringency
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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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