Class GenomicIndexUtil


  • public class GenomicIndexUtil
    extends Object
    Constants and methods used by BAM and Tribble indices
    • 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.