C# Class 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.

Inheritance: ISequence, IQualitativeSequence

Afficher le fichier Open project: dotnetbio/bio Class Usage Examples

Méthodes publiques

Свойство	Type	Description
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[]

Méthodes publiques

Méthode	Description
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

Private Methods

Méthode	Description
System ( ) : System.Collections.IEnumerator

Method Details

GetComplementedSequence() public méthode

public GetComplementedSequence ( ) : ISequence
Résultat	ISequence

GetEncodedQualityScore() public méthode

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

GetEncodedQualityScores() public méthode

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

GetEnumerator() public méthode

public GetEnumerator ( ) : IEnumerator
Résultat	IEnumerator

GetReverseComplementedSequence() public méthode

public GetReverseComplementedSequence ( ) : ISequence
Résultat	ISequence

GetReversedSequence() public méthode

public GetReversedSequence ( ) : ISequence
Résultat	ISequence

GetSubSequence() public méthode

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

IndexOfNonGap() public méthode

public IndexOfNonGap ( ) : long
Résultat	long

IndexOfNonGap() public méthode

public IndexOfNonGap ( long startPos ) : long
startPos	long
Résultat	long

LastIndexOfNonGap() public méthode

public LastIndexOfNonGap ( ) : long
Résultat	long

LastIndexOfNonGap() public méthode

public LastIndexOfNonGap ( long endPos ) : long
endPos	long
Résultat	long

PacBioCCSRead() public méthode

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.
Résultat	System

this() public méthode

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

Property Details

AvgZscore public_oe property

The average Z-score for all subreads.

public float AvgZscore
Résultat	float

Barcode1 public_oe property

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

public ushort Barcode1
Résultat	ushort

Barcode2 public_oe property

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

public ushort Barcode2
Résultat	ushort

HoleNumber public_oe property

What is the hole number for the ZMW.

public int HoleNumber
Résultat	int

Movie public_oe property

The name of the movie this CCS read came from.

public string Movie
Résultat	string

MutationsApplied public_oe property

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

public int MutationsApplied
Résultat	int

MutationsTested public_oe property

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

public int MutationsTested
Résultat	int

NumPasses public_oe property

The number of subreads that were used to generate the consensus sequence.

public int NumPasses
Résultat	int

ProcessingTimeMS public_oe property

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
Résultat	float

ReadGroup public_oe property

The read group.

public string ReadGroup
Résultat	string

ReadQuality public_oe property

A measure of CCS read quality

public float ReadQuality
Résultat	float

Sequence public_oe property

The consensus sequence and associated QV values.

public QualitativeSequence,Bio Sequence
Résultat	Bio.QualitativeSequence

SnrA public_oe property

The SNR of the A Channel

public float SnrA
Résultat	float

SnrC public_oe property

The SNR of the C Channel

public float SnrC
Résultat	float

SnrG public_oe property

The SNR of the G Channel

public float SnrG
Résultat	float

SnrT public_oe property

The SNR of the T Channel

public float SnrT
Résultat	float

ZScores public_oe property

An array of Z-scores for each subread added. Subreads that were not added are report as Double.NaN values.

public float[] ZScores
Résultat	float[]