FastQParser Class

FastQParser Class

A FastQParser reads from a source of text that is formatted according to the FASTQ file specification and converts the data to in-memory QualitativeSequence objects.

Inheritance Hierarchy

SystemObject
Bio.IO.FastQFastQParser

Namespace: Bio.IO.FastQ
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

C++

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public class FastQParser : IParserWithAlphabet<IQualitativeSequence>, 
	IParser<IQualitativeSequence>, IParser

Public Class FastQParser
	Implements IParserWithAlphabet(Of IQualitativeSequence), IParser(Of IQualitativeSequence), 
	IParser

public ref class FastQParser : IParserWithAlphabet<IQualitativeSequence^>, 
	IParser<IQualitativeSequence^>, IParser

type FastQParser =  
    class
        interface IParserWithAlphabet<IQualitativeSequence>
        interface IParser<IQualitativeSequence>
        interface IParser
    end

The FastQParser type exposes the following members.

Constructors

	Name	Description
	FastQParser	Initializes a new instance of the FastQParser class.

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Properties

	Name	Description
	Alphabet	Gets or sets the alphabet to use for parsed ISequence objects. If this is not set, the alphabet will be determined based on the file being parsed.
	Description	Gets the description of the parser. This is intended to give developers some information of the parser class. This property returns a simple description of what this class achieves.
	FormatType	Gets or sets the format type to be used. The FastQFormatType to be used for parsed QualitativeSequence objects. Default value is Illumina_v1_8
	Name	Gets the type of parser. This is intended to give developers name of the parser.
	SupportedFileTypes	Gets a comma separated values of the possible FastQ file extensions.

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Methods

	Name	Description
	Equals	Determines whether the specified object is equal to the current object. (Inherited from Object.)
	Finalize	Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.)
	GetHashCode	Serves as the default hash function. (Inherited from Object.)
	GetType	Gets the Type of the current instance. (Inherited from Object.)
	MemberwiseClone	Creates a shallow copy of the current Object. (Inherited from Object.)
	Parse	Gets the IEnumerable of QualitativeSequences from the steam being parsed.
	ParseOne(Stream)	Returns a single QualitativeSequence from the FASTQ data.
	ParseOne(Stream, FastQFormatType)	Returns a single QualitativeSequence from the FASTQ data.
	ToString	Returns a string that represents the current object. (Inherited from Object.)

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Reference

Bio.IO.FastQ Namespace