htsjdk.samtools

Interface SamReader.Indexing

All Known Implementing Classes:

CRAMFileReader, SamReader.PrimitiveSamReaderToSamReaderAdapter, SRAFileReader

Enclosing interface:

SamReader

public static interface SamReader.Indexing

Facet for index-related operations.

Method Summary

Modifier and Type	Method and Description
BrowseableBAMIndex	getBrowseableIndex() Gets an index tagged with the BrowseableBAMIndex interface.
SAMFileSpan	getFilePointerSpanningReads() Gets a pointer spanning all reads in the BAM file.
BAMIndex	getIndex() Retrieves the index for the given file type.
boolean	hasBrowseableIndex() Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.
SAMRecordIterator	iterator(SAMFileSpan chunks) Iterate through the given chunks in the file.

Method Detail

getIndex

BAMIndex getIndex()

Retrieves the index for the given file type. Ensure that the index is of the specified type.

Returns:

An index of the given type.

hasBrowseableIndex

boolean hasBrowseableIndex()

Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.

Returns:

True if the index supports the BrowseableBAMIndex interface. False otherwise.

getBrowseableIndex

BrowseableBAMIndex getBrowseableIndex()

Gets an index tagged with the BrowseableBAMIndex interface. Throws an exception if no such index is available.

Returns:

An index with a browseable interface, if possible.

Throws:

SAMException - if no such index is available.

iterator

SAMRecordIterator iterator(SAMFileSpan chunks)

Iterate through the given chunks in the file.

Parameters:

chunks - List of chunks for which to retrieve data.

Returns:

An iterator over the given chunks.

getFilePointerSpanningReads

SAMFileSpan getFilePointerSpanningReads()

Gets a pointer spanning all reads in the BAM file.

Returns:

Unbounded pointer to the first record, in chunk format.