All Superinterfaces:

AutoCloseable, Closeable

All Known Subinterfaces:

BrowseableBAMIndex

All Known Implementing Classes:

AbstractBAMFileIndex, CSIIndex, DiskBasedBAMFileIndex, SRAIndex
```
public interface BAMIndex
extends Closeable
```
A basic interface for querying BAM indices.

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`BAI_INDEX_SUFFIX`	Deprecated. since June 2019 Use `FileExtensions.BAI_INDEX` instead.
`static String`	`BAMIndexSuffix`	Deprecated. since June 2019 Use `FileExtensions.BAI_INDEX` instead.
`static String`	`CSI_INDEX_SUFFIX`	Deprecated. since June 2019 Use `FileExtensions.CSI` instead.

Method Summary

All Methods Instance Methods Abstract Methods
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.

- Field Detail
  - BAMIndexSuffix
```
@Deprecated
static final String BAMIndexSuffix
```
    Deprecated.
    since June 2019 Use FileExtensions.BAI_INDEX instead.
    
    See Also:
    
    Constant Field Values
  - BAI_INDEX_SUFFIX
```
@Deprecated
static final String BAI_INDEX_SUFFIX
```
    Deprecated.
    since June 2019 Use FileExtensions.BAI_INDEX instead.
    
    See Also:
    
    Constant Field Values
  - CSI_INDEX_SUFFIX
```
@Deprecated
static final String CSI_INDEX_SUFFIX
```
    Deprecated.
    since June 2019 Use FileExtensions.CSI instead.
    
    See Also:
    
    Constant Field Values
- Method Detail
  - getSpanOverlapping
```
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. See the BAM spec for more information on how a chunk is represented.
    
    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
```
long getStartOfLastLinearBin()
```
    Gets the start of the last linear bin in the index.
    
    Returns:
    
    The chunk indicating the start of the last bin in the linear index.
  - getMetaData
```
BAMIndexMetaData getMetaData(int reference)
```
    Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
    
    Parameters:
    
    reference - the reference of interest
    
    Returns:
    
    meta data for the reference
  - close
```
void close()
```
    Close the index and release any associated resources.
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable

Interface BAMIndex

Field Summary

Method Summary

Field Detail

BAMIndexSuffix

BAI_INDEX_SUFFIX

CSI_INDEX_SUFFIX

Method Detail

getSpanOverlapping

getStartOfLastLinearBin

getMetaData

close