public class SRAFileReader extends SamReader.ReaderImplementation implements SamReader.Indexing
| Constructor and Description |
|---|
SRAFileReader(SRAAccession acc) |
| Modifier and Type | Method and Description |
|---|---|
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() |
public SRAFileReader(SRAAccession acc)
public SamReader.Type type()
type in interface SamReader.PrimitiveSamReaderpublic boolean hasIndex()
hasIndex in interface SamReader.PrimitiveSamReaderpublic BAMIndex getIndex()
SamReader.IndexinggetIndex in interface SamReader.IndexinggetIndex in interface SamReader.PrimitiveSamReaderpublic SAMFileHeader getFileHeader()
getFileHeader in interface SamReader.PrimitiveSamReaderpublic CloseableIterator<SAMRecord> getIterator()
getIterator in interface SamReader.PrimitiveSamReaderpublic CloseableIterator<SAMRecord> getIterator(SAMFileSpan chunks)
getIterator in interface SamReader.PrimitiveSamReaderpublic SAMFileSpan getFilePointerSpanningReads()
SamReader.IndexinggetFilePointerSpanningReads in interface SamReader.IndexinggetFilePointerSpanningReads in interface SamReader.PrimitiveSamReaderpublic CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)
query in interface SamReader.PrimitiveSamReaderpublic CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence, int start)
queryAlignmentStart in interface SamReader.PrimitiveSamReaderpublic CloseableIterator<SAMRecord> queryUnmapped()
queryUnmapped in interface SamReader.PrimitiveSamReaderpublic void close()
close in interface SamReader.PrimitiveSamReaderpublic ValidationStringency getValidationStringency()
getValidationStringency in interface SamReader.PrimitiveSamReaderpublic boolean hasBrowseableIndex()
hasBrowseableIndex in interface SamReader.Indexingpublic BrowseableBAMIndex getBrowseableIndex()
getBrowseableIndex in interface SamReader.IndexingSAMException - if no such index is available.public SAMRecordIterator iterator(SAMFileSpan chunks)
iterator in interface SamReader.Indexingchunks - List of chunks for which to retrieve data.protected SRAIterator.RecordRangeInfo getRecordsRangeInfo()