SRAIndex (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.SRAIndex

All Implemented Interfaces:

BAMIndex, BrowseableBAMIndex, java.io.Closeable, java.lang.AutoCloseable
```
public class SRAIndex
extends java.lang.Object
implements BrowseableBAMIndex
```
Emulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works: SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as a length of all references. Reading unaligned reads is then fast if we use read positions for lookup and (internally) filter out aligned fragments. Total SRA "file" range is calculated as sum of all reference lengths plus number of reads (both aligned and unaligned) in SRA archive. Now, we can use Chunks to lookup for aligned and unaligned fragments. We emulate BAM index bins by mapping SRA reference positions to bin numbers. And then we map from bin number to list of chunks, which represent SRA "file" positions (which are simply reference positions). We only emulate last level of BAM index bins (and they refer to a portion of reference SRA_BIN_SIZE bases long). For all other bins RuntimeException will be returned (but since nobody else creates bins, except SRAIndex class that is fine). But since the last level of bins was not meant to refer to fragments that only partially overlap bin reference positions, we also return chunk that goes 5000 bases left before beginning of the bin to assure fragments that start before the bin positions but still overlap with it can be retrieved by SRA reader. Later we will add support to NGS API to get a maximum number of bases that we need to go left to retrieve such fragments. Created by andrii.nikitiuk on 9/4/15.

Field Summary

Fields
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

Fields inherited from interface htsjdk.samtools.BAMIndex
BAMIndexSuffix

Constructor Summary

Constructors
Constructor and Description

SRAIndex(SAMFileHeader header, SRAIterator.RecordRangeInfo recordRangeInfo)

Constructors
Constructor and Description
`SRAIndex(SAMFileHeader header, SRAIterator.RecordRangeInfo recordRangeInfo)`

Method Summary

All Methods Instance Methods Concrete Methods
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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SRA_BIN_SIZE
```
public static final int SRA_BIN_SIZE
```
    Number of reference bases bins in last level can represent
    
    See Also:
    
    Constant Field Values
  - SRA_CHUNK_SIZE
```
public static final int SRA_CHUNK_SIZE
```
    Chunks of that size will be created when using SRA index
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SRAIndex
```
public SRAIndex(SAMFileHeader header,
                SRAIterator.RecordRangeInfo recordRangeInfo)
```
    Parameters:
    
    header - sam header
    
    recordRangeInfo - info about record ranges withing SRA archive
- Method Detail
  - getLevelSize
```
public int getLevelSize(int levelNumber)
```
    Gets the size (number of bins in) a given level of a BAM index.
    
    Specified by:
    
    getLevelSize in interface BrowseableBAMIndex
    
    Parameters:
    
    levelNumber - Level for which to inspect the size.
    
    Returns:
    
    Size of the given level.
  - getLevelForBin
```
public int getLevelForBin(Bin bin)
```
    SRA only operates on bins from last level
    
    Specified by:
    
    getLevelForBin in interface BrowseableBAMIndex
    
    Parameters:
    
    bin - The bin for which to determine the level.
    
    Returns:
    
    bin level
  - getFirstLocusInBin
```
public int getFirstLocusInBin(Bin bin)
```
    Gets the first locus that this bin can index into.
    
    Specified by:
    
    getFirstLocusInBin in interface BrowseableBAMIndex
    
    Parameters:
    
    bin - The bin to test.
    
    Returns:
    
    first position that associated with given bin number
  - getLastLocusInBin
```
public int getLastLocusInBin(Bin bin)
```
    Gets the last locus that this bin can index into.
    
    Specified by:
    
    getLastLocusInBin in interface BrowseableBAMIndex
    
    Parameters:
    
    bin - The bin to test.
    
    Returns:
    
    last position that associated with given bin number
  - getBinsOverlapping
```
public BinList getBinsOverlapping(int referenceIndex,
                                  int startPos,
                                  int endPos)
```
    Provides a list of bins that contain bases at requested positions
    
    Specified by:
    
    getBinsOverlapping in interface BrowseableBAMIndex
    
    Parameters:
    
    referenceIndex - sequence of desired SAMRecords
    
    startPos - 1-based start of the desired interval, inclusive
    
    endPos - 1-based end of the desired interval, inclusive
    
    Returns:
    
    a list of bins that contain relevant data
  - getSpanOverlapping
```
public BAMFileSpan getSpanOverlapping(Bin bin)
```
    Description copied from interface: BrowseableBAMIndex
    
    Perform an overlapping query of all bins bounding the given location.
    
    Specified by:
    
    getSpanOverlapping in interface BrowseableBAMIndex
    
    Parameters:
    
    bin - The bin over which to perform an overlapping query.
    
    Returns:
    
    The file pointers
  - getSpanOverlapping
```
public BAMFileSpan getSpanOverlapping(int referenceIndex,
                                      int startPos,
                                      int endPos)
```
    Description copied from interface: BAMIndex
    
    Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive. See the BAM spec for more information on how a chunk is represented.
    
    Specified by:
    
    getSpanOverlapping in interface BAMIndex
    
    Parameters:
    
    referenceIndex - The contig.
    
    startPos - Genomic start of query.
    
    endPos - Genomic end of query.
    
    Returns:
    
    A file span listing the chunks in the BAM file.
  - getStartOfLastLinearBin
```
public long getStartOfLastLinearBin()
```
    Description copied from interface: BAMIndex
    
    Gets the start of the last linear bin in the index.
    
    Specified by:
    
    getStartOfLastLinearBin in interface BAMIndex
    
    Returns:
    
    a position where aligned fragments end
  - getMetaData
```
public BAMIndexMetaData getMetaData(int reference)
```
    Description copied from interface: BAMIndex
    
    Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
    
    Specified by:
    
    getMetaData in interface BAMIndex
    
    Parameters:
    
    reference - the reference of interest
    
    Returns:
    
    meta data for the reference
  - close
```
public void close()
```
    Description copied from interface: BAMIndex
    
    Close the index and release any associated resources.
    
    Specified by:
    
    close in interface BAMIndex
    
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable

Class SRAIndex

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SRA_BIN_SIZE

SRA_CHUNK_SIZE

Constructor Detail

SRAIndex

Method Detail

getLevelSize

getLevelForBin

getFirstLocusInBin

getLastLocusInBin

getBinsOverlapping

getSpanOverlapping

getSpanOverlapping

getStartOfLastLinearBin

getMetaData

close