picard.analysis

Class GcBiasUtils

java.lang.Object

picard.analysis.GcBiasUtils

public class GcBiasUtils
extends java.lang.Object

Utilities to calculate GC Bias Created by kbergin on 9/23/15.

Constructor Summary

Constructors

Constructor and Description
GcBiasUtils()

Method Summary

Modifier and Type	Method and Description
static byte[]	calculateAllGcs(byte[] refBases, int lastWindowStart, int windowSize)
static int	calculateGc(byte[] bases, int startIndex, int endIndex, picard.analysis.GcBiasUtils.CalculateGcState state)
static int[]	calculateRefWindowsByGc(int windows, java.io.File referenceSequence, int windowSize)

Methods inherited from class java.lang.Object

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

Constructor Detail

GcBiasUtils

public GcBiasUtils()

Method Detail

calculateGc

public static int calculateGc(byte[] bases,
                              int startIndex,
                              int endIndex,
                              picard.analysis.GcBiasUtils.CalculateGcState state)

calculateRefWindowsByGc

public static int[] calculateRefWindowsByGc(int windows,
                                            java.io.File referenceSequence,
                                            int windowSize)

calculateAllGcs

public static byte[] calculateAllGcs(byte[] refBases,
                                     int lastWindowStart,
                                     int windowSize)