SAMFormatter Class

SAMFormatter Class

Writes a SequenceAlignmentMap to a particular location, usually a file. The output is formatted according to the SAM file format specification 1.4. A method is also provided for quickly accessing the content in string form for applications that do not need to first write to file. Documentation for the latest SAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

Inheritance Hierarchy

SystemObject
Bio.IO.SAMSAMFormatter

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

Syntax

C++

Copy

public class SAMFormatter : ISequenceAlignmentFormatter, 
	IFormatter<ISequenceAlignment>, IFormatter

Public Class SAMFormatter
	Implements ISequenceAlignmentFormatter, IFormatter(Of ISequenceAlignment), 
	IFormatter

public ref class SAMFormatter : ISequenceAlignmentFormatter, 
	IFormatter<ISequenceAlignment^>, IFormatter

type SAMFormatter =  
    class
        interface ISequenceAlignmentFormatter
        interface IFormatter<ISequenceAlignment>
        interface IFormatter
    end

The SAMFormatter type exposes the following members.

Constructors

	Name	Description
	SAMFormatter	Initializes a new instance of the SAMFormatter class

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Properties

	Name	Description
	Description	Gets the description of the sequence alignment formatter being implemented. This is intended to give the developer some information of the formatter.
	Name	Gets the name of the sequence alignment formatter being implemented. This is intended to give the developer some information of the formatter type.
	SupportedFileTypes	Gets the file extensions that the formatter implementation will support.

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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.)
	Format(Stream, ISequenceAlignment)	Writes an ISequenceAlignment to the location specified by the stream.
	Format(Stream, IEnumerableISequenceAlignment)	Write a collection of ISequenceAlignments to a file.
	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.)
	ToString	Returns a string that represents the current object. (Inherited from Object.)
	WriteHeader	Writes specified SAMAlignedHeader to specified text writer.
	WriteSAMAlignedSequence	Writes SAMAlignedSequence to specified text writer.

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Reference

Bio.IO.SAM Namespace