Package org.snpeff.binseq

Class DnaAndQualitySequence

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaAndQualitySequence

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BinarySequence>

Direct Known Subclasses:

DnaAndQualitySequenceWithId

public class DnaAndQualitySequence
extends BinarySequence

Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , .. , 63] - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'bytes'

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DnaAndQualitySequence(java.lang.String seqStr)
DnaAndQualitySequence(java.lang.String seqStr, java.lang.String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)
DnaAndQualitySequence(org.biojava.nbio.genome.io.fastq.Fastq fastq)

Method Summary

Modifier and Type	Method	Description
int	compareTo(BinarySequence o)
static DnaAndQualitySequence	empty()
char	getBase(int index)	Return the base at position 'index'
int	getCode(int index)	Return the code at position 'index'
Coder	getCoder()	Get sequence encoder & decoder
byte[]	getCodes()
java.lang.String	getQuality()	Get quality string (encoded FastQ-Sanger style)
int	getQuality(int index)
java.lang.String	getSequence()	Get the sequence as a String
int	hashCode()
int	indexOf(java.lang.String seq)	Find the position of 'seq' in this sequence
int	lastIndexOf(java.lang.String seq)	Returns the index within this string of the rightmost occurrence of the specified substring
int	length()	Sequence lenth
DnaAndQualitySequence	overlap(BinarySequence sequence, int start)	Creates a new sequence by overlapping 'this' and 'sequence' E.g.
DnaAndQualitySequence	read(java.io.DataInputStream dataInStream)	Read data in binary format
protected void	readDataStream(java.io.DataInputStream dataInStream)	Read data in binary format
DnaAndQualitySequence	reverseWc()	Reverse Watson-Cricks complement
void	set(java.lang.String seqStr)	Set sequence
void	set(java.lang.String seqStr, java.lang.String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)	Set sequence
java.lang.String	toString()
void	write(java.io.DataOutputStream dataOutStream)	Write data in binary format

Methods inherited from class org.snpeff.binseq.BinarySequence

clone, setQuality

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

DnaAndQualitySequence

public DnaAndQualitySequence(org.biojava.nbio.genome.io.fastq.Fastq fastq)

DnaAndQualitySequence

public DnaAndQualitySequence(java.lang.String seqStr)

DnaAndQualitySequence

public DnaAndQualitySequence(java.lang.String seqStr,
                             java.lang.String qualityStr,
                             org.biojava.nbio.genome.io.fastq.FastqVariant type)

Method Detail

empty

public static DnaAndQualitySequence empty()

compareTo

public int compareTo(BinarySequence o)

getBase

public char getBase(int index)

Description copied from class: BinarySequence

Return the base at position 'index'

Overrides:

getBase in class BinarySequence

getCode

public int getCode(int index)

Description copied from class: BinarySequence

Return the code at position 'index'

Specified by:

getCode in class BinarySequence

getCoder

public Coder getCoder()

Description copied from class: BinarySequence

Get sequence encoder & decoder

Specified by:

getCoder in class BinarySequence

getCodes

public byte[] getCodes()

getQuality

public java.lang.String getQuality()

Get quality string (encoded FastQ-Sanger style)

Returns:

getQuality

public int getQuality(int index)

getSequence

public java.lang.String getSequence()

Description copied from class: BinarySequence

Get the sequence as a String

Specified by:

getSequence in class BinarySequence

hashCode

public int hashCode()

Specified by:

hashCode in class BinarySequence

indexOf

public int indexOf(java.lang.String seq)

Find the position of 'seq' in this sequence

Parameters:

seq - : String to be found

Returns:

The position where 'seq' is found or '-1' if not found

lastIndexOf

public int lastIndexOf(java.lang.String seq)

Returns the index within this string of the rightmost occurrence of the specified substring

length

public int length()

Sequence lenth

Specified by:

length in class BinarySequence

Returns:

overlap

public DnaAndQualitySequence overlap(BinarySequence sequence,
                                     int start)

Creates a new sequence by overlapping 'this' and 'sequence' E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO | other.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| this.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO | |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| Another case is when a sequence is fully included in the other sequence. In this case the result is just a copy of the longest sequence (with the quality updated) E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| other.sequence : | OOOOOOOOOOOOOOO | | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| this.sequence : | OOOOOOOOOOO | other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO| |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO|

Overrides:

overlap in class BinarySequence

Parameters:

start -

Returns:

A new sequence

read

public DnaAndQualitySequence read(java.io.DataInputStream dataInStream)
                           throws java.io.IOException

Read data in binary format

Specified by:

read in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException

readDataStream

protected void readDataStream(java.io.DataInputStream dataInStream)
                       throws java.io.IOException

Read data in binary format

Specified by:

readDataStream in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException

reverseWc

public DnaAndQualitySequence reverseWc()

Description copied from class: BinarySequence

Reverse Watson-Cricks complement

Specified by:

reverseWc in class BinarySequence

set

public void set(java.lang.String seqStr)

Set sequence

Specified by:

set in class BinarySequence

Parameters:

seqStr -

set

public void set(java.lang.String seqStr,
                java.lang.String qualityStr,
                org.biojava.nbio.genome.io.fastq.FastqVariant type)

Set sequence

Parameters:

seqStr -

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

write

public void write(java.io.DataOutputStream dataOutStream)
           throws java.io.IOException

Write data in binary format

Specified by:

write in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException