CRAMFileReader
, SamReader.PrimitiveSamReaderToSamReaderAdapter
, SRAFileReader
public static interface SamReader.Indexing
Modifier and Type | Method | Description |
---|---|---|
BrowseableBAMIndex |
getBrowseableIndex() |
Gets an index tagged with the BrowseableBAMIndex interface.
|
SAMFileSpan |
getFilePointerSpanningReads() |
Gets a pointer spanning all reads in the BAM file.
|
BAMIndex |
getIndex() |
Retrieves the index for the given file type.
|
boolean |
hasBrowseableIndex() |
Returns true if the supported index is browseable, meaning the bins in it can be traversed
and chunk data inspected and retrieved.
|
SAMRecordIterator |
iterator(SAMFileSpan chunks) |
Iterate through the given chunks in the file.
|
BAMIndex getIndex()
boolean hasBrowseableIndex()
BrowseableBAMIndex getBrowseableIndex()
SAMException
- if no such index is available.SAMRecordIterator iterator(SAMFileSpan chunks)
chunks
- List of chunks for which to retrieve data.SAMFileSpan getFilePointerSpanningReads()