Package org.snpeff.binseq.coder

Class DnaCoder

java.lang.Object

org.snpeff.binseq.coder.Coder

org.snpeff.binseq.coder.DnaCoder

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

DnaQualityCoder

public class DnaCoder
extends Coder

Class used to encode & decode sequences into binary and vice-versa Note:This is a singleton class. It stores DNA bases into 2 bits {a,c,g,t} <-> {0,1,2,3}

Author:

pcingola

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected static int	BASES_PER_LONGWORD
protected static int	BITS_PER_BASE
int[]	COUNT_DIFFS
static boolean	debug
protected static int	LAST_BASE_IN_LONGWORD
static long	MASK_ALL_WORD
long[]	MASK_BASE
protected static long	MASK_FIRST_BASE
long[]	MASK_HIGH
long[]	MASK_LOW
static char[]	TO_BASE

Fields inherited from class org.snpeff.binseq.coder.Coder

BITS_PER_LONGWORD, BYTES_PER_LONGWORD

Method Summary

Modifier and Type	Method	Description
int	basesPerWord()	How many bases can we pack in a word
int	baseToBits(char c)	Encode a base using 2 bits
int	baseToBits(char c, boolean ignoreErrors)
int	bitsPerBase()	How many bits do we need for each base
void	copyBases(long[] src, int srcStart, long[] dst, int dstStart, int length)	Copy 'length' bases from 'src' (starting from 'srcStart') to 'dst' (starting from 'dstStart')
void	copyBases(long[] src, long[] dst, int start, int length)	Copy 'length' bases from 'src' to 'dst' (starting from 'start')
int	decodeWord(long word, int pos)	Decode bits from a given position
long	encodeWord(char base, int pos)	Encode a base to a given position in a word
static DnaCoder	get()
int	lastBaseinWord()	Index of the last base coded in a word
int	length2words(int len)	Calculate the coded length of a sequence in 'words' (depends on coder)
long	mask(int baseIndexInWord)	Bitmask for a base in a word
long	replaceBase(long code, int pos, char newBase)	Decode bits from a given position
long	reverseBases(long code)	Reverse all bases in 'code'
int	score(long[] dst, long[] src, int srcStart, int length, int threshold)	Calculate a 'score' for a sequence (dst) and a sub-sequence (src).
char	toBase(int code)	Decode a base using 2 bits
char	toBase(long word, int pos)	Decode a base from a given position in a word

Methods inherited from class org.snpeff.binseq.coder.Coder

qualityToBits, toQuality

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static boolean debug

BITS_PER_BASE

protected static final int BITS_PER_BASE

See Also:

Constant Field Values

MASK_FIRST_BASE

protected static final long MASK_FIRST_BASE

See Also:

Constant Field Values

BASES_PER_LONGWORD

protected static final int BASES_PER_LONGWORD

See Also:

Constant Field Values

LAST_BASE_IN_LONGWORD

protected static final int LAST_BASE_IN_LONGWORD

See Also:

Constant Field Values

MASK_ALL_WORD

public static final long MASK_ALL_WORD

See Also:

Constant Field Values

TO_BASE

public static final char[] TO_BASE

MASK_BASE

public long[] MASK_BASE

MASK_LOW

public long[] MASK_LOW

MASK_HIGH

public long[] MASK_HIGH

COUNT_DIFFS

public int[] COUNT_DIFFS

Method Detail

get

public static DnaCoder get()

basesPerWord

public int basesPerWord()

Description copied from class: Coder

How many bases can we pack in a word

Specified by:

basesPerWord in class Coder

Returns:

baseToBits

public int baseToBits(char c)

Encode a base using 2 bits

Specified by:

baseToBits in class Coder

Parameters:

c -

Returns:

baseToBits

public int baseToBits(char c,
                      boolean ignoreErrors)

bitsPerBase

public int bitsPerBase()

Description copied from class: Coder

How many bits do we need for each base

Specified by:

bitsPerBase in class Coder

Returns:

copyBases

public void copyBases(long[] src,
                      int srcStart,
                      long[] dst,
                      int dstStart,
                      int length)

Copy 'length' bases from 'src' (starting from 'srcStart') to 'dst' (starting from 'dstStart')

Parameters:

src -

srcStart -

dst -

length -

copyBases

public void copyBases(long[] src,
                      long[] dst,
                      int start,
                      int length)

Copy 'length' bases from 'src' to 'dst' (starting from 'start')

Parameters:

src -

start -

dst -

length -

decodeWord

public int decodeWord(long word,
                      int pos)

Decode bits from a given position

Specified by:

decodeWord in class Coder

Parameters:

word -

pos -

Returns:

encodeWord

public long encodeWord(char base,
                       int pos)

Encode a base to a given position in a word

Parameters:

base -

pos -

Returns:

lastBaseinWord

public int lastBaseinWord()

Description copied from class: Coder

Index of the last base coded in a word

Specified by:

lastBaseinWord in class Coder

Returns:

length2words

public int length2words(int len)

Calculate the coded length of a sequence in 'words' (depends on coder)

Parameters:

len -

Returns:

mask

public long mask(int baseIndexInWord)

Description copied from class: Coder

Bitmask for a base in a word

Specified by:

mask in class Coder

Returns:

replaceBase

public long replaceBase(long code,
                        int pos,
                        char newBase)

Decode bits from a given position

Parameters:

code -

pos -

Returns:

reverseBases

public long reverseBases(long code)

Reverse all bases in 'code'

Parameters:

linearIndex -

Returns:

score

public int score(long[] dst,
                 long[] src,
                 int srcStart,
                 int length,
                 int threshold)

Calculate a 'score' for a sequence (dst) and a sub-sequence (src). The score is the number of equal bases (or zero if they differ)

Parameters:

dst - : Destination sequence codes[]

src - : Source sequence codes[]

srcStart - : Source sub-sequence start

length - : Number of bases to compare

threshold - : Number of bases allowed to differ

Returns:

toBase

public char toBase(int code)

Decode a base using 2 bits

Specified by:

toBase in class Coder

Returns:

toBase

public char toBase(long word,
                   int pos)

Description copied from class: Coder

Decode a base from a given position in a word

Specified by:

toBase in class Coder

Returns: