org.broadinstitute.hellbender.utils

Class BaseUtils

java.lang.Object

org.broadinstitute.hellbender.utils.BaseUtils

public final class BaseUtils
extends java.lang.Object

BaseUtils contains some basic utilities for manipulating nucleotides.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BaseUtils.Base
static class	BaseUtils.BaseSubstitutionType

Field Summary

Fields

Modifier and Type	Field and Description
static char[]	BASE_CHARS
static byte[]	BASES
static java.util.Comparator<byte[]>	BASES_COMPARATOR Lexicographical sorting of base arrays Comparator.

Method Summary

Modifier and Type	Method and Description
static byte	baseIndexToSimpleBase(int baseIndex) Converts a base index to a simple base
static boolean	basesAreEqual(byte base1, byte base2)
static byte	basesToIUPAC(byte base1, byte base2) Converts a pair of bases to their IUPAC ambiguity code
static byte[]	convertIUPACtoN(byte[] bases, boolean errorOnBadReferenceBase, boolean ignoreConversionOfFirstByte)
static void	fillWithRandomBases(byte[] dest, int fromIndex, int toIndex) Fill an array section with random bases.
static byte	getComplement(byte base)
static boolean	isAllRegularBases(byte[] bases) Returns true iff all bases are 'regular' isRegularBase(byte).
static boolean	isNBase(byte base)
static boolean	isRegularBase(byte base) Returns true iff the base represented by the byte is a 'regular' base (ACGT or *).
static boolean	isTransition(byte base1, byte base2)
static int	simpleBaseToBaseIndex(byte base) Converts a simple base to a base index
static byte	simpleComplement(byte base) Return the complement (A <-> T or C <-> G) of a base, or the specified base if it can't be complemented (i.e.
static byte[]	simpleReverseComplement(byte[] bases) Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
static BaseUtils.BaseSubstitutionType	SNPSubstitutionType(byte base1, byte base2) Returns the base substitution type of the 2 state SNP

Methods inherited from class java.lang.Object

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

Field Detail

BASES

public static final byte[] BASES

BASE_CHARS

public static final char[] BASE_CHARS

BASES_COMPARATOR

public static final java.util.Comparator<byte[]> BASES_COMPARATOR

Lexicographical sorting of base arrays Comparator.

Method Detail

isNBase

public static boolean isNBase(byte base)

SNPSubstitutionType

public static BaseUtils.BaseSubstitutionType SNPSubstitutionType(byte base1,
                                                                 byte base2)

Returns the base substitution type of the 2 state SNP

Parameters:

base1 -

base2 -

Returns:

isTransition

public static boolean isTransition(byte base1,
                                   byte base2)

basesAreEqual

public static boolean basesAreEqual(byte base1,
                                    byte base2)

convertIUPACtoN

public static byte[] convertIUPACtoN(byte[] bases,
                                     boolean errorOnBadReferenceBase,
                                     boolean ignoreConversionOfFirstByte)

simpleBaseToBaseIndex

public static int simpleBaseToBaseIndex(byte base)

Converts a simple base to a base index

Parameters:

base - [AaCcGgTt]

Returns:

0, 1, 2, 3, or -1 if the base can't be understood

isRegularBase

public static boolean isRegularBase(byte base)

Returns true iff the base represented by the byte is a 'regular' base (ACGT or *).

isAllRegularBases

public static boolean isAllRegularBases(byte[] bases)

Returns true iff all bases are 'regular' isRegularBase(byte).

baseIndexToSimpleBase

public static byte baseIndexToSimpleBase(int baseIndex)

Converts a base index to a simple base

Parameters:

baseIndex - 0, 1, 2, 3

Returns:

A, C, G, T, or '.' if the index can't be understood

simpleComplement

public static byte simpleComplement(byte base)

Return the complement (A <-> T or C <-> G) of a base, or the specified base if it can't be complemented (i.e. an ambiguous base).

Parameters:

base - the base [AaCcGgTt]

Returns:

the complementary base, or the input base if it's not one of the understood ones

simpleReverseComplement

public static byte[] simpleReverseComplement(byte[] bases)

Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)

Parameters:

bases - the byte array of bases

Returns:

the reverse complement of the base byte array

fillWithRandomBases

public static void fillWithRandomBases(byte[] dest,
                                       int fromIndex,
                                       int toIndex)

Fill an array section with random bases.

Parameters:

dest - array to fill.

fromIndex - first index to be filled (inclusive).

toIndex - index after last to be filled (exclusive).

Throws:

java.lang.IllegalArgumentException - if dest is null, fromIndex or toIndex is negative, fromIndex or toIndex are greater than dest length, or fromIndex greater than toIndex.

getComplement

public static byte getComplement(byte base)

basesToIUPAC

public static byte basesToIUPAC(byte base1,
                                byte base2)

Converts a pair of bases to their IUPAC ambiguity code

Parameters:

base1 - 1st base

base2 - 2nd base

Returns:

byte