Package htsjdk.samtools

Interface BAMIndex

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 Details

  • Method Details

    • 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