public class SRAFileReader extends SamReader.ReaderImplementation implements SamReader.Indexing
Constructor and Description |
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SRAFileReader(SRAAccession acc) |
Modifier and Type | Method and Description |
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void |
close() |
BrowseableBAMIndex |
getBrowseableIndex()
Gets an index tagged with the BrowseableBAMIndex interface.
|
SAMFileHeader |
getFileHeader() |
SAMFileSpan |
getFilePointerSpanningReads()
Gets a pointer spanning all reads in the BAM file.
|
BAMIndex |
getIndex()
Retrieves the index for the given file type.
|
CloseableIterator<SAMRecord> |
getIterator() |
CloseableIterator<SAMRecord> |
getIterator(SAMFileSpan chunks) |
protected SRAIterator.RecordRangeInfo |
getRecordsRangeInfo() |
ValidationStringency |
getValidationStringency() |
boolean |
hasBrowseableIndex()
Returns true if the supported index is browseable, meaning the bins in it can be traversed
and chunk data inspected and retrieved.
|
boolean |
hasIndex() |
SAMRecordIterator |
iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
CloseableIterator<SAMRecord> |
query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
queryUnmapped() |
SamReader.Type |
type() |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
isQueryable
public SRAFileReader(SRAAccession acc)
public SamReader.Type type()
type
in interface SamReader.PrimitiveSamReader
public boolean hasIndex()
hasIndex
in interface SamReader.PrimitiveSamReader
public BAMIndex getIndex()
SamReader.Indexing
getIndex
in interface SamReader.Indexing
getIndex
in interface SamReader.PrimitiveSamReader
public SAMFileHeader getFileHeader()
getFileHeader
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> getIterator()
getIterator
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> getIterator(SAMFileSpan chunks)
getIterator
in interface SamReader.PrimitiveSamReader
public SAMFileSpan getFilePointerSpanningReads()
SamReader.Indexing
getFilePointerSpanningReads
in interface SamReader.Indexing
getFilePointerSpanningReads
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)
query
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence, int start)
queryAlignmentStart
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> queryUnmapped()
queryUnmapped
in interface SamReader.PrimitiveSamReader
public void close()
close
in interface SamReader.PrimitiveSamReader
public ValidationStringency getValidationStringency()
getValidationStringency
in interface SamReader.PrimitiveSamReader
public boolean hasBrowseableIndex()
hasBrowseableIndex
in interface SamReader.Indexing
public BrowseableBAMIndex getBrowseableIndex()
getBrowseableIndex
in interface SamReader.Indexing
SAMException
- if no such index is available.public SAMRecordIterator iterator(SAMFileSpan chunks)
iterator
in interface SamReader.Indexing
chunks
- List of chunks for which to retrieve data.protected SRAIterator.RecordRangeInfo getRecordsRangeInfo()