Package htsjdk.samtools

Class GenomicIndexUtil

java.lang.Object
htsjdk.samtools.GenomicIndexUtil
public class GenomicIndexUtil extends Object
Constants and methods used by BAM and Tribble indices

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    BIN_GENOMIC_SPAN
    Reports the total amount of genomic data that any bin can index.
    static final int[]
    LEVEL_STARTS
    What is the starting bin for each level?
    static final int
    MAX_BINS
    Reports the maximum number of bins that can appear in a binning index.
    static final int
    MAX_LINEAR_INDEX_SIZE
     
    static final int
    UNSET_GENOMIC_LOCATION
    E.g.

  • Constructor Summary

    Constructors
    Constructor
    Description
    GenomicIndexUtil()
     

  • Method Summary

    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

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • BIN_GENOMIC_SPAN

      public static final int BIN_GENOMIC_SPAN
      Reports the total amount of genomic data that any bin can index.
      See Also:

    • 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:

    • 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:

  • Constructor Details

    • GenomicIndexUtil

      public GenomicIndexUtil()

  • Method Details

    • 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.