net.maizegenetics.dna.snp.score

Class AlleleDepthUtil

java.lang.Object

net.maizegenetics.dna.snp.score.AlleleDepthUtil

public class AlleleDepthUtil
extends Object

Depth compression utility. Depths are scored in byte (256 states). 0 to 127 are used for exact depth values. -128 to -1 are used for log approximations (1.0746^(-x)). This permits depths upto 10,482 to be stored with exact precision for low values, and <3% error for high depths.

Author:

Terry Casstevens, Robert Bukowski

Field Summary

Fields

Modifier and Type	Field and Description
static byte	DEPTH_BYTE_MISSING
static int	DEPTH_MISSING

Method Summary

Modifier and Type	Method and Description
static byte	addByteDepths(byte depth1, byte depth2) Returns the depth combined depths in byte format.
static int	depthByteToInt(byte depth) Converts byte depth to integer version.
static int[]	depthByteToInt(byte[] depth) Converts byte arrays of depth to integer array version.
static byte	depthIntToByte(int depth) Converts integer depth to byte version.
static byte[]	depthIntToByte(int[] depth) Converts integer array of depth to byte array version.
static byte[][]	depthIntToByte(int[][] depth) Converts a two dimensional integer array of depths to a 2D byte array version.

Methods inherited from class java.lang.Object

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

Field Detail

DEPTH_BYTE_MISSING

public static final byte DEPTH_BYTE_MISSING

See Also:

Constant Field Values

DEPTH_MISSING

public static final int DEPTH_MISSING

See Also:

Constant Field Values

Method Detail

addByteDepths

public static byte addByteDepths(byte depth1,
                                 byte depth2)

Returns the depth combined depths in byte format. Converts both to integers, adds, and reconverts back.

Parameters:

depth1 - first depth in byte format

depth2 - second depth in byte format

Returns:

byte version of combined depth

depthIntToByte

public static byte depthIntToByte(int depth)

Converts integer depth to byte version. Positive return values are exact, negative return values are log approximations

depthIntToByte

public static byte[] depthIntToByte(int[] depth)

Converts integer array of depth to byte array version. Positive return values are exact, negative return values are log approximations

depthIntToByte

public static byte[][] depthIntToByte(int[][] depth)

Converts a two dimensional integer array of depths to a 2D byte array version. Positive return values are exact, negative return values are log approximations

depthByteToInt

public static int depthByteToInt(byte depth)

Converts byte depth to integer version. Positive depths value are exact, negative depths are log approximations

depthByteToInt

public static int[] depthByteToInt(byte[] depth)

Converts byte arrays of depth to integer array version. Positive depths value are exact, negative depths are log approximations