public interface BAMIndex
extends java.io.Closeable
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
BAMIndexSuffix |
| Modifier and Type | Method and 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 java.lang.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 java.lang.AutoCloseableclose in interface java.io.Closeable