HS.SDA3.GenomicsVariant
hidden serial class HS.SDA3.GenomicsVariant extends HS.SDA3.DataType
One line of a VCF file. When we store SDA, we only extract the small subset of variants that are clinically significant. The properties are taken from the VCF spec (columns 1-6)Property Inventory
Properties
property ALT as %String;
Alternate base(s): Comma separated list of alternate non-reference alleles called on at least one of the
samples. Options are base strings made up of the bases A,C,G,T,N,* (case insensitive) or an angle-bracketed
ID string ("") or a breakend replacement string.
Property methods: ALTDisplayToLogical(), ALTGet(), ALTIsValid(), ALTLogicalToDisplay(), ALTLogicalToOdbc(), ALTNormalize(), ALTSet()
property CHROM as %String;
Chromosome: An identifier from the reference genome or an angle-bracketed ID String (")
pointing to a contig in the assembly file. No colons or white space permitted
Property methods: CHROMDisplayToLogical(), CHROMGet(), CHROMIsValid(), CHROMLogicalToDisplay(), CHROMLogicalToOdbc(), CHROMNormalize(), CHROMSet()
property Extension as HS.Local.SDA3.GenomicsVariantExtension;
Property methods: ExtensionGet(), ExtensionGetObject(), ExtensionGetObjectId(), ExtensionGetSwizzled(), ExtensionIsEmpty(), ExtensionIsValid(), ExtensionNewObject(), ExtensionSet(), ExtensionSetObject(), ExtensionSetObjectId(), ExtensionUnSwizzle()
property ID as %String;
ID - identifier: Semi-colon separated list of unique identifiers where available. If this is a
dbSNP (single nucleotide pair) variant it is encouraged to use the rs number(s). No identifier should
be present in more than one data record.
TBD: We think these comments mean that CHROM+POS+ID is like a primary key for the row
Property methods: IDDisplayToLogical(), IDGet(), IDIsValid(), IDLogicalToDisplay(), IDLogicalToOdbc(), IDNormalize(), IDSet()
property POS as HS.SDA3.Numeric;
Position: The reference position, with the 1st base having position 1. It is permitted to have
multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N
is the lenght of the corresponding chromosome or contig
Property methods: POSDisplayToLogical(), POSGet(), POSIsValid(), POSLogicalToDisplay(), POSNormalize(), POSSet(), POSXSDToLogical()
property QUAL as HS.SDA3.Numeric;
Quality: Phred-scaled quality score for the assertion made in ALT. i.e. - -10Log10 prob(call in ALT is wrong)
Property methods: QUALDisplayToLogical(), QUALGet(), QUALIsValid(), QUALLogicalToDisplay(), QUALNormalize(), QUALSet(), QUALXSDToLogical()
property REF as %String;
Reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted.
The value in the POS field refers to the position of the first base in the String.
Property methods: REFDisplayToLogical(), REFGet(), REFIsValid(), REFLogicalToDisplay(), REFLogicalToOdbc(), REFNormalize(), REFSet()
Inherited Members
Inherited Methods
- %AddToSaveSet()
- %AddToSyncSet()
- %ClassIsLatestVersion()
- %ClassName()
- %ConstructClone()
- %Delete()
- %DeleteId()
- %DispatchClassMethod()
- %DispatchGetModified()
- %DispatchGetProperty()
- %DispatchMethod()
- %DispatchSetModified()
- %DispatchSetMultidimProperty()
- %DispatchSetProperty()
- %Extends()
- %GetParameter()
- %GetSwizzleObject()
- %IsA()
- %IsModified()
- %IsNull()
- %New()
- %NormalizeObject()
- %ObjectIsNull()
- %ObjectModified()
- %OnBeforeAddToSync()
- %OnDetermineClass()
- %Open()
- %OpenId()
- %OriginalNamespace()
- %PackageName()
- %RemoveFromSaveSet()
- %ResolveConcurrencyConflict()
- %SerializeObject()
- %SetModified()
- %SyncObjectIn()
- %SyncTransport()
- %ValidateObject()
- IsDefined()
- LogIgnoredTag()
- LogicalToOdbc()
- OdbcToLogical()
- ToQuickXML()
- ToQuickXMLStream()
- ToQuickXMLString()
- Translate()
- UpdateSDA()
- XMLDTD()
- XMLExport()
- XMLExportToStream()
- XMLExportToString()
- XMLImportSDAString()
- XMLImportSDAStringUnknown()
- XMLNew()
- XMLSchema()
- XMLSchemaNamespace()
- XMLSchemaType()