Package htsjdk.samtools.util

Class CoordMath

java.lang.Object
htsjdk.samtools.util.CoordMath
public class CoordMath extends Object
Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends inclusive.

  • Constructor Summary

    Constructors
    Constructor
    Description
    CoordMath()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean
    encloses(int outerStart, int outerEnd, int innerStart, int innerEnd)
    Returns true if the "inner" coords and totally enclosed by the "outer" coords.
    static int
    getCycle(boolean isNegativeStrand, int readLength, int readBaseIndex)
    Determines the read cycle number for the base
    static int
    getEnd(int start, int length)
     
    static int
    getLength(int start, int end)
     
    static int
    getOverlap(int start, int end, int start2, int end2)
    Determines the amount of overlap between two coordinate ranges.
    static int
    getStart(int end, int length)
     
    static boolean
    overlaps(int start, int end, int start2, int end2)
    Checks to see if the two sets of coordinates have any overlap.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • CoordMath

      public CoordMath()

  • Method Details

    • getLength

      public static int getLength(int start, int end)

    • getStart

      public static int getStart(int end, int length)

    • getEnd

      public static int getEnd(int start, int length)

    • overlaps

      public static boolean overlaps(int start, int end, int start2, int end2)
      Checks to see if the two sets of coordinates have any overlap.

    • encloses

      public static boolean encloses(int outerStart, int outerEnd, int innerStart, int innerEnd)
      Returns true if the "inner" coords and totally enclosed by the "outer" coords.

    • getOverlap

      public static int getOverlap(int start, int end, int start2, int end2)
      Determines the amount of overlap between two coordinate ranges. Assumes that the two ranges actually do overlap and therefore may produce strange results when they do not!

    • getCycle

      public static int getCycle(boolean isNegativeStrand, int readLength, int readBaseIndex)
      Determines the read cycle number for the base
      Parameters:
      isNegativeStrand - true if the read is negative strand
      readLength -
      readBaseIndex - the 0-based index of the read base in question