public class SRAIterator extends java.lang.Object implements SAMRecordIterator
Modifier and Type | Class and Description |
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static class |
SRAIterator.RecordRangeInfo
Describes record ranges info needed for emulating BAM index
|
Constructor and Description |
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SRAIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
java.util.List<Chunk> chunks) |
Modifier and Type | Method and 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.
|
static SRAIterator.RecordRangeInfo |
getRecordsRangeInfo(ngs.ReadCollection run)
Loads record ranges needed for emulating BAM index
|
boolean |
hasNext()
NGS iterators implement a single method "nextObject" which return true if the operation was successful or
false if there are no more objects available.
|
SAMRecord |
next()
Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from
one of them.
|
void |
remove() |
void |
setValidationStringency(ValidationStringency validationStringency) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public SRAIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, java.util.List<Chunk> chunks)
run
- opened read collectionheader
- sam headercachedReferences
- list of cached references shared among all iterators from a single SRAFileReaderrecordRangeInfo
- info about record ranges withing SRA archivechunks
- used to determine which records the iterator should returnpublic static SRAIterator.RecordRangeInfo getRecordsRangeInfo(ngs.ReadCollection run)
run
- read collectionpublic boolean hasNext()
hasNext
in interface java.util.Iterator<SAMRecord>
public SAMRecord next()
next
in interface java.util.Iterator<SAMRecord>
public void remove()
remove
in interface java.util.Iterator<SAMRecord>
public void close()
CloseableIterator
close
in interface CloseableIterator<SAMRecord>
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
SAMRecordIterator
assertSorted
in interface SAMRecordIterator
sortOrder
- The order in which records are expected to be returnedpublic void setValidationStringency(ValidationStringency validationStringency)