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Class TSequenceVariant

Description
Hierarchy
Fields
Methods
Properties

Unit

bsFhir_stu3

Declaration

type TSequenceVariant = class(TBackboneElement)

Description

Raw data describing a biological sequence.

Hierarchy

Overview

Methods

Public constructor Create; override;

Properties

Public property start : integer read Getstart write Setstart;
Public property startElement : Tinteger read GetstartElement write SetstartElement;
Public property end_ : integer read Getend_ write Setend_;
Public property end_Element : Tinteger read Getend_Element write Setend_Element;
Public property observedAllele : string read GetobservedAllele write SetobservedAllele;
Public property observedAlleleElement : Tstring read GetobservedAlleleElement write SetobservedAlleleElement;
Public property referenceAllele : string read GetreferenceAllele write SetreferenceAllele;
Public property referenceAlleleElement : Tstring read GetreferenceAlleleElement write SetreferenceAlleleElement;
Public property cigar : string read Getcigar write Setcigar;
Public property cigarElement : Tstring read GetcigarElement write SetcigarElement;
Public property variantPointer : TReference read GetvariantPointer write SetvariantPointer;

Description

Methods

Public constructor Create; override;
 

Properties

Public property start : integer read Getstart write Setstart;

Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Public property startElement : Tinteger read GetstartElement write SetstartElement;
 
Public property end_ : integer read Getend_ write Setend_;

End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Public property end_Element : Tinteger read Getend_Element write Setend_Element;
 
Public property observedAllele : string read GetobservedAllele write SetobservedAllele;

An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Public property observedAlleleElement : Tstring read GetobservedAlleleElement write SetobservedAlleleElement;
 
Public property referenceAllele : string read GetreferenceAllele write SetreferenceAllele;

An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Public property referenceAlleleElement : Tstring read GetreferenceAlleleElement write SetreferenceAlleleElement;
 
Public property cigar : string read Getcigar write Setcigar;

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).

Public property cigarElement : Tstring read GetcigarElement write SetcigarElement;
 
Public property variantPointer : TReference read GetvariantPointer write SetvariantPointer;

A pointer to an Observation containing variant information.

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