C# 클래스 Bio.IO.PacBio.PacBioCCSRead

A class representing the consensus sequence generated from multiple subreads. This is produced by the program pbccs and output to a BAM file.
상속: ISequence, IQualitativeSequence
파일 보기 프로젝트 열기: dotnetbio/bio 1 사용 예제들

공개 프로퍼티들

프로퍼티 타입 설명
AvgZscore float
Barcode1 ushort
Barcode2 ushort
HoleNumber int
Movie string
MutationsApplied int
MutationsTested int
NumPasses int
ProcessingTimeMS float
ReadGroup string
ReadQuality float
Sequence Bio.QualitativeSequence
SnrA float
SnrC float
SnrG float
SnrT float
ZScores float[]

공개 메소드들

메소드 설명
GetComplementedSequence ( ) : ISequence
GetEncodedQualityScore ( long index ) : byte
GetEncodedQualityScores ( ) : byte[]
GetEnumerator ( ) : IEnumerator
GetReverseComplementedSequence ( ) : ISequence
GetReversedSequence ( ) : ISequence
GetSubSequence ( long start, long length ) : ISequence
IndexOfNonGap ( ) : long
IndexOfNonGap ( long startPos ) : long
LastIndexOfNonGap ( ) : long
LastIndexOfNonGap ( long endPos ) : long
PacBioCCSRead ( Bio.IO.SAM.SAMAlignedSequence s ) : System

Initializes a new instance of the Bio.IO.PacBio.PacBioCCSRead class. From an initially parsed BAM file.
this ( long index ) : byte

비공개 메소드들

메소드 설명
System ( ) : System.Collections.IEnumerator

메소드 상세

GetComplementedSequence() 공개 메소드

public GetComplementedSequence ( ) : ISequence
리턴 ISequence

GetEncodedQualityScore() 공개 메소드

public GetEncodedQualityScore ( long index ) : byte
index long
리턴 byte

GetEncodedQualityScores() 공개 메소드

public GetEncodedQualityScores ( ) : byte[]
리턴 byte[]

GetEnumerator() 공개 메소드

public GetEnumerator ( ) : IEnumerator
리턴 IEnumerator

GetReverseComplementedSequence() 공개 메소드

public GetReverseComplementedSequence ( ) : ISequence
리턴 ISequence

GetReversedSequence() 공개 메소드

public GetReversedSequence ( ) : ISequence
리턴 ISequence

GetSubSequence() 공개 메소드

public GetSubSequence ( long start, long length ) : ISequence
start long
length long
리턴 ISequence

IndexOfNonGap() 공개 메소드

public IndexOfNonGap ( ) : long
리턴 long

IndexOfNonGap() 공개 메소드

public IndexOfNonGap ( long startPos ) : long
startPos long
리턴 long

LastIndexOfNonGap() 공개 메소드

public LastIndexOfNonGap ( ) : long
리턴 long

LastIndexOfNonGap() 공개 메소드

public LastIndexOfNonGap ( long endPos ) : long
endPos long
리턴 long

PacBioCCSRead() 공개 메소드

Initializes a new instance of the Bio.IO.PacBio.PacBioCCSRead class. From an initially parsed BAM file.
public PacBioCCSRead ( Bio.IO.SAM.SAMAlignedSequence s ) : System
s Bio.IO.SAM.SAMAlignedSequence S.
리턴 System

this() 공개 메소드

public this ( long index ) : byte
index long
리턴 byte

프로퍼티 상세

AvgZscore 공개적으로 프로퍼티

The average Z-score for all subreads.
public float AvgZscore
리턴 float

Barcode1 공개적으로 프로퍼티

The first barcode found. Only available if CCS is built with DIAGNOSTICS defined and the file contained barcodes.
public ushort Barcode1
리턴 ushort

Barcode2 공개적으로 프로퍼티

The second barcode found. Only available if CCS is built with DIAGNOSTICS defined and the file contained barcodes.
public ushort Barcode2
리턴 ushort

HoleNumber 공개적으로 프로퍼티

What is the hole number for the ZMW.
public int HoleNumber
리턴 int

Movie 공개적으로 프로퍼티

The name of the movie this CCS read came from.
public string Movie
리턴 string

MutationsApplied 공개적으로 프로퍼티

The number of mutations applied during polishing. Only available if CCS is built with DIAGNOSTICS defined.
public int MutationsApplied
리턴 int

MutationsTested 공개적으로 프로퍼티

The number of mutations tested during polishing. Only available if CCS is built with DIAGNOSTICS defined.
public int MutationsTested
리턴 int

NumPasses 공개적으로 프로퍼티

The number of subreads that were used to generate the consensus sequence.
public int NumPasses
리턴 int

ProcessingTimeMS 공개적으로 프로퍼티

The amount of time it took to process the ZMW to generate consensus. Only available if CCS is built with DIAGNOSTICS defined.
public float ProcessingTimeMS
리턴 float

ReadGroup 공개적으로 프로퍼티

The read group.
public string ReadGroup
리턴 string

ReadQuality 공개적으로 프로퍼티

A measure of CCS read quality
public float ReadQuality
리턴 float

Sequence 공개적으로 프로퍼티

The consensus sequence and associated QV values.
public QualitativeSequence,Bio Sequence
리턴 Bio.QualitativeSequence

SnrA 공개적으로 프로퍼티

The SNR of the A Channel
public float SnrA
리턴 float

SnrC 공개적으로 프로퍼티

The SNR of the C Channel
public float SnrC
리턴 float

SnrG 공개적으로 프로퍼티

The SNR of the G Channel
public float SnrG
리턴 float

SnrT 공개적으로 프로퍼티

The SNR of the T Channel
public float SnrT
리턴 float

ZScores 공개적으로 프로퍼티

An array of Z-scores for each subread added. Subreads that were not added are report as Double.NaN values.
public float[] ZScores
리턴 float[]