Package 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 Details

    • 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.