SAMAlignedSequence Class

Class to hold Reads or aligned sequence or query sequence in SAM Alignment.

Inheritance Hierarchy

SystemObject
Bio.IO.SAMSAMAlignedSequence

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

Syntax

public class SAMAlignedSequence : IAlignedSequence

Public Class SAMAlignedSequence
	Implements IAlignedSequence

public ref class SAMAlignedSequence : IAlignedSequence

type SAMAlignedSequence =  
    class
        interface IAlignedSequence
    end

The SAMAlignedSequence type exposes the following members.

Constructors

	Name	Description
	SAMAlignedSequence	Creates new instance of SAMAlignedSequence.
	SAMAlignedSequence(SAMAlignedSequenceHeader)	Creates new instance of SAMAlignedSequence with specified SAMAlignedSequenceHeader.

Properties

	Name	Description
	Bin	Gets bin depending on POS and CIGAR values.
	CIGAR	Extended CIGAR string.
	Flag	SAM flags. SAMFlags
	IsDummyRead	Is this read a special dummy read? These read types are a special type in later BAM file formats that are designed to hold annotation data. They are identified as having SEQ set to *, FLAG bits 0x100 and 0x200 set (secondary and filtered), and a CT tag.
	ISize	Inferred insert size.
	MapQ	Mapping quality (phred-scaled posterior probability that the mapping position of this read is incorrect).
	Metadata	Metadata of this aligned sequence. SAMAlignedSequenceHeader is stored with the key "SAMAlignedSequenceHeader".
	MPos	One-based leftmost mate position of the clipped sequence.
	MRNM	Mate reference sequence name.
	OptionalFields	Optional fields.
	Pos	One-based leftmost position/coordinate of the clipped sequence.
	QName	Query pair name if paired; or Query name if unpaired.
	QuerySequence	Gets or sets read/query/aligned sequence.
	RefEndPos	Gets one based alignment end position of reference sequence depending on CIGAR Value.
	RName	Reference sequence name.
	Sequences	Always returns QuerySequence in a 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.)
	GetEncodedQualityScores	Gets encoded quality scores.
	GetHashCode	Serves as the default hash function. (Inherited from Object.)
	GetQualityScores	Gets Phred base quality scores.
	GetType	Gets the Type of the current instance. (Inherited from Object.)
	MemberwiseClone	Creates a shallow copy of the current Object. (Inherited from Object.)
	SetPreValidatedCIGAR	Set a pre-validated extended cigar string, the alignment length and bin are still calculated
	SetPreValidatedMRNM	Set the mate reference sequence name assuming the value is already valid.
	SetPreValidatedRName	Sets the RName using a name that has already been validated as valid, and so does not need to be checked against the regular expression.
	ToString	Returns a string that represents the current object. (Inherited from Object.)