SequenceAlignmentMap Class

Class to hold sequence alignment map (SAM) structure.

Inheritance Hierarchy

SystemObject
Bio.IO.SAMSequenceAlignmentMap

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

Syntax

public class SequenceAlignmentMap : ISequenceAlignment

Public Class SequenceAlignmentMap
	Implements ISequenceAlignment

public ref class SequenceAlignmentMap : ISequenceAlignment

type SequenceAlignmentMap =  
    class
        interface ISequenceAlignment
    end

The SequenceAlignmentMap type exposes the following members.

Constructors

	Name	Description
	SequenceAlignmentMap	Default constructor. Creates SequenceAlignmentMap instance.
	SequenceAlignmentMap(SAMAlignmentHeader)	Creates SequenceAlignmentMap instance.

Properties

	Name	Description
	AlignedSequences	Gets list of aligned sequences present in this alignment.
	Documentation	Gets documentation object.
	Header	Gets the SAM header.
	Metadata	Gets the metadata of this alignment.
	QuerySequences	Gets the query sequences present in this alignment.
	Sequences	Gets list of source sequences present in this alignment. Note that this method always returns an empty list.

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.)
	GetPairedReads	Gets the paired reads.
	GetPairedReads(String)	Gets the paired reads.
	GetPairedReads(CloneLibraryInformation)	Gets the paired reads.
	GetPairedReads(Single, Single)	Gets the paired reads.
	GetReferenceSequenceRanges	Returns list of SequenceRanges objects which represents reference sequences present in the header.
	GetRefSequences	Returns list of reference sequences present in this header.
	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.)