public class SRAIndex extends java.lang.Object implements BrowseableBAMIndex
| Modifier and Type | Field and Description |
|---|---|
static int |
SRA_BIN_SIZE
Number of reference bases bins in last level can represent
|
static int |
SRA_CHUNK_SIZE
Chunks of that size will be created when using SRA index
|
BAMIndexSuffix| Constructor and Description |
|---|
SRAIndex(SAMFileHeader header,
SRAIterator.RecordRangeInfo recordRangeInfo) |
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Close the index and release any associated resources.
|
BinList |
getBinsOverlapping(int referenceIndex,
int startPos,
int endPos)
Provides a list of bins that contain bases at requested positions
|
int |
getFirstLocusInBin(Bin bin)
Gets the first locus that this bin can index into.
|
int |
getLastLocusInBin(Bin bin)
Gets the last locus that this bin can index into.
|
int |
getLevelForBin(Bin bin)
SRA only operates on bins from last level
|
int |
getLevelSize(int levelNumber)
Gets the size (number of bins in) a given level of a BAM index.
|
BAMIndexMetaData |
getMetaData(int reference)
Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
|
BAMFileSpan |
getSpanOverlapping(Bin bin)
Perform an overlapping query of all bins bounding the given location.
|
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.
|
public static final int SRA_BIN_SIZE
public static final int SRA_CHUNK_SIZE
public SRAIndex(SAMFileHeader header, SRAIterator.RecordRangeInfo recordRangeInfo)
header - sam headerrecordRangeInfo - info about record ranges withing SRA archivepublic int getLevelSize(int levelNumber)
getLevelSize in interface BrowseableBAMIndexlevelNumber - Level for which to inspect the size.public int getLevelForBin(Bin bin)
getLevelForBin in interface BrowseableBAMIndexbin - The bin for which to determine the level.public int getFirstLocusInBin(Bin bin)
getFirstLocusInBin in interface BrowseableBAMIndexbin - The bin to test.public int getLastLocusInBin(Bin bin)
getLastLocusInBin in interface BrowseableBAMIndexbin - The bin to test.public BinList getBinsOverlapping(int referenceIndex, int startPos, int endPos)
getBinsOverlapping in interface BrowseableBAMIndexreferenceIndex - sequence of desired SAMRecordsstartPos - 1-based start of the desired interval, inclusiveendPos - 1-based end of the desired interval, inclusivepublic BAMFileSpan getSpanOverlapping(Bin bin)
BrowseableBAMIndexgetSpanOverlapping in interface BrowseableBAMIndexbin - The bin over which to perform an overlapping query.public BAMFileSpan getSpanOverlapping(int referenceIndex, int startPos, int endPos)
BAMIndexgetSpanOverlapping in interface BAMIndexreferenceIndex - The contig.startPos - Genomic start of query.endPos - Genomic end of query.public long getStartOfLastLinearBin()
BAMIndexgetStartOfLastLinearBin in interface BAMIndexpublic BAMIndexMetaData getMetaData(int reference)
BAMIndexgetMetaData in interface BAMIndexreference - the reference of interest