AutoCloseable
, Closeable
BrowseableBAMIndex
AbstractBAMFileIndex
, DiskBasedBAMFileIndex
, SRAIndex
public interface BAMIndex extends Closeable
Modifier and Type | Field | Description |
---|---|---|
static String |
BAMIndexSuffix |
Modifier and Type | Method | Description |
---|---|---|
void |
close() |
Close the index and release any associated resources.
|
BAMIndexMetaData |
getMetaData(int reference) |
Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
|
BAMFileSpan |
getSpanOverlapping(int referenceIndex,
int startPos,
int endPos) |
Gets the compressed chunks which should be searched for the contents of records contained by the span
referenceIndex:startPos-endPos, inclusive.
|
long |
getStartOfLastLinearBin() |
Gets the start of the last linear bin in the index.
|
static final String BAMIndexSuffix
BAMFileSpan getSpanOverlapping(int referenceIndex, int startPos, int endPos)
referenceIndex
- The contig.startPos
- Genomic start of query.endPos
- Genomic end of query.long getStartOfLastLinearBin()
BAMIndexMetaData getMetaData(int reference)
reference
- the reference of interestvoid close()
close
in interface AutoCloseable
close
in interface Closeable