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

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Public Properties

Property	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[]

Public Methods

Method	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

Method	Description
System ( ) : System.Collections.IEnumerator

Method Details

GetComplementedSequence() public method

public GetComplementedSequence ( ) : ISequence
return	ISequence

GetEncodedQualityScore() public method

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

GetEncodedQualityScores() public method

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

GetEnumerator() public method

public GetEnumerator ( ) : IEnumerator
return	IEnumerator

GetReverseComplementedSequence() public method

public GetReverseComplementedSequence ( ) : ISequence
return	ISequence

GetReversedSequence() public method

public GetReversedSequence ( ) : ISequence
return	ISequence

GetSubSequence() public method

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

IndexOfNonGap() public method

public IndexOfNonGap ( ) : long
return	long

IndexOfNonGap() public method

public IndexOfNonGap ( long startPos ) : long
startPos	long
return	long

LastIndexOfNonGap() public method

public LastIndexOfNonGap ( ) : long
return	long

LastIndexOfNonGap() public method

public LastIndexOfNonGap ( long endPos ) : long
endPos	long
return	long

PacBioCCSRead() public method

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.
return	System

this() public method

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

Property Details

AvgZscore public_oe property

The average Z-score for all subreads.

public float AvgZscore
return	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
return	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
return	ushort

HoleNumber public_oe property

What is the hole number for the ZMW.

public int HoleNumber
return	int

Movie public_oe property

The name of the movie this CCS read came from.

public string Movie
return	string

MutationsApplied public_oe property

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

public int MutationsApplied
return	int

MutationsTested public_oe property

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

public int MutationsTested
return	int

NumPasses public_oe property

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

public int NumPasses
return	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
return	float

ReadGroup public_oe property

The read group.

public string ReadGroup
return	string

ReadQuality public_oe property

A measure of CCS read quality

public float ReadQuality
return	float

Sequence public_oe property

The consensus sequence and associated QV values.

public QualitativeSequence,Bio Sequence
return	Bio.QualitativeSequence

SnrA public_oe property

The SNR of the A Channel

public float SnrA
return	float

SnrC public_oe property

The SNR of the C Channel

public float SnrC
return	float

SnrG public_oe property

The SNR of the G Channel

public float SnrG
return	float

SnrT public_oe property

The SNR of the T Channel

public float SnrT
return	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
return	float[]