Field Detail

• BIN_GENOMIC_SPAN

  public static final int BIN_GENOMIC_SPAN

  Reports the total amount of genomic data that any bin can index.

  See Also:

  Constant Field Values

• LEVEL_STARTS

  public static final int[] LEVEL_STARTS

  What is the starting bin for each level?

• MAX_BINS

  public static final int MAX_BINS

  Reports the maximum number of bins that can appear in a binning index.

  See Also:

  Constant Field Values

• MAX_LINEAR_INDEX_SIZE

  public static final int MAX_LINEAR_INDEX_SIZE

• UNSET_GENOMIC_LOCATION

  public static final int UNSET_GENOMIC_LOCATION

  E.g. for a SAMRecord with no genomic coordinate.

  See Also:

  Constant Field Values

Constructor Detail

• GenomicIndexUtil

  public GenomicIndexUtil()

Method Detail

• regionToBin

  public static int regionToBin​(int beg,
                                int end)

  calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "

  Parameters:

  beg - 0-based start of read (inclusive)

  end - 0-based end of read (exclusive)

• regionToBins

  public static BitSet regionToBins​(int startPos,
                                    int endPos)

  Get candidate bins for the specified region

  Parameters:

  startPos - 1-based start of target region, inclusive.

  endPos - 1-based end of target region, inclusive.

  Returns:

  bit set for each bin that may contain SAMRecords in the target region.