Package htsjdk.samtools

Class GenomicIndexUtil

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

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static int binTolevel​(int bin)
      Return the binning index level for the given bin.
      static String getBinSummaryString​(int bin)
      Return a summary string describing the bin level, level size, and genomic territory covered by the bin.
      static int levelToSize​(int level)
      Return the binning index bin size for bins in the given bin.
      static int regionToBin​(int beg, int end)
      calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC.
      static int regionToBin​(int beg, int end, int minShift, int binDepth)
      calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC.
      static BitSet regionToBins​(int startPos, int endPos)
      Get candidate bins for the specified region
      static BitSet regionToBins​(int startPos, int endPos, int minShift, int binDepth)
      Get candidate bins for the specified region

    • 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

      • binTolevel

        public static int binTolevel​(int bin)
        Return the binning index level for the given bin. Assumes a .bai/.tbi binning scheme (not for use with .csi).
        Parameters:
        bin - the bin to analyze
        Returns:
        the binning index level for the given bin

      • levelToSize

        public static int levelToSize​(int level)
        Return the binning index bin size for bins in the given bin. Assumes a .bai/.tbi binning scheme (not for use with .csi).
        Parameters:
        level - the level to analyze
        Returns:
        the size for a bin at the given level

      • getBinSummaryString

        public static String getBinSummaryString​(int bin)
        Return a summary string describing the bin level, level size, and genomic territory covered by the bin. For use as debug output.
        Parameters:
        bin - input bin
        Returns:
        A summary string describing the bin. The intended use is for debug output - the string is not intended to be machine readable/parsed and is subject to change.

      • 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)

      • regionToBin

        public static int regionToBin​(int beg,
                              int end,
                              int minShift,
                              int binDepth)
        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)
        minShift - minimum bin width (2^minShift)
        binDepth - number of levels in the binning scheme (including bin 0)

      • 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.

      • regionToBins

        public static BitSet regionToBins​(int startPos,
                                  int endPos,
                                  int minShift,
                                  int binDepth)
        Get candidate bins for the specified region
        Parameters:
        startPos - 1-based start of target region, inclusive.
        endPos - 1-based end of target region, inclusive.
        minShift - minimum bin width (2^minShift).
        binDepth - number of levels in the binning scheme (including bin 0).
        Returns:
        bit set for each bin that may contain SAMRecords in the target region.