ajvardata

Enum AjEVarType

Enumerated value(s)

Name
AJVAR_UNKNOWN	Unknown
AJVAR_INT	Integer
AJVAR_FLOAT	Float
AJVAR_CHAR	Character
AJVAR_STR	String
AJVAR_FLAG	Flag (INFO, not FORMAT)
AJVAR_MAX	Above last defined value

Data type AjPVarHeader

Holds the metadata definitions for variation data

Based on the requirements for VCF format 4.1

Alias name(s)

Name
AjSVarHeader
AjOVarHeader

Attributes

Name	Type	Description
Header	AjPList	Tag-value list of general header records
Fields	AjPList	List of VarField definitions (INFO and FORMAT)
Samples	AjPList	List of VarSample definitions
Filters	AjPList	List of Filter tag-value definitions
Alts	AjPList	List of Alternate tag-value definitions
Pedigrees	AjPList	List of Pedigree tag-value definitions
SampleIds	AjPList	List of SampleID strings from column headings
RefseqIds	AjPTable	Table of reference sequence name-id pairs

Data type AjPVarField

Holds the metadata definitions for variation data fields

Based on the requirements for VCF format 4.1

Alias name(s)

Name
AjSVarField
AjOVarField

Attributes

Name	Type	Description
Field	AjPStr	Field name (INFO, FILTER, FORMAT)
Id	AjPStr	Identifier
Desc	AjPStr	Description
Type	AjEVarType	Type of value
Number	ajint	Count of values

Data type AjPVarSample

Holds the metadata definitions for variation data samples

Based on the requirements for VCF format 4.1

Alias name(s)

Name
AjSVarSample
AjOVarSample

Attributes

Name	Type	Description
Id	AjPStr	Identifier
Desc	AjPStr*	Descriptions for each genome identifier
Genomes	AjPStr*	Genome identifiers
Mixture	float*	Mixture proportions, summing to 1.0
Number	ajuint	Count of genome identifiers
Padding	ajuint	Padding to alignment boundary

Data type AjPVarData

Holds the metadata definitions for variation data records

Based on the requirements for VCF format 4.1

Alias name(s)

Name
AjSVarAlt
AjOVarAlt

Attributes

Name	Type	Description
Chrom	AjPStr	Chromosome
Id	AjPStr	Identifier
Ref	AjPStr	Reference sequence(s)
Alt	AjPStr	Alternate sequence(s)
Qual	AjPStr	Quality
Filter	AjPStr	Filter(s) failed
Info	AjPStr	Info field metadata
Format	AjPStr	Format field metadata
Samples	AjPList	Sample string records
Pos	ajuint	Position
Padding	ajuint	Padding to alignment boundary

Data type AjPVar

Holds the variation itself, plus associated information.

Alias name(s)

Name
AjSVar
AjOVar

Attributes

Name	Type	Description
Id	AjPStr	Id of term
Db	AjPStr	Database name from input
Setdb	AjPStr	Database name from command line
Full	AjPStr	Full name
Qry	AjPStr	Query for re-reading
Formatstr	AjPStr	Input format name
Filename	AjPStr	Original filename
Textptr	AjPStr	Full text
Data	AjPList	Data records as AjPVarData objects
Header	AjPVarHeader	Header record metadata
Fpos	ajlong	File position
Format	AjEnum	Input format enum
Hasdata	AjBool	True when data has been loaded

Data type AjPVarin

Holds the input specification and information needed to read the variation and possible further entries

Alias name(s)

Name
AjSVarin
AjOVarin

Attributes

Name	Type	Description
Input	AjPTextin	General text input object
Begin	ajint	Start position
End	ajint	End position
Loading	AjBool	True if data is now loading
Padding	char[4]	Padding to alignment boundary
VarData	void*	Format data for reuse, e.g. multiple term input (unused in current code)

Data type AjPVarload

Inherits an AjPVar but allows more variations to be read from the same input by also inheriting the AjPVarin input object.

Alias name(s)

Name
AjSVarload
AjOVarload

Attributes

Name	Type	Description
Var	AjPVar	Current variation
Varin	AjPVarin	Variation input for reading next
Count	ajuint	Count of terms so far
Loading	AjBool	True if data is now loading
Returned	AjBool	if true: Variation object has been returned to a new owner and is not to be deleted by the destructor
Padding	ajuint	Padding to alignment boundary

Data type AjPVarall

Inherits an AjPVar but allows more variations to be read from the same input by also inheriting the AjPVarin input object.

Alias name(s)

Name
AjSVarall
AjOVarall

Attributes

Name	Type	Description
Loader	AjPVarload	Variation loader for reading next
Totterms	ajulong	Count of terms so far
Count	ajuint	Count of terms so far
Multi	AjBool	True if multiple values are expected
Returned	AjBool	if true: Variation object has been returned to a new owner and is not to be deleted by the destructor
Padding	ajuint	Padding to alignment boundary

Data type AjPVarAccess

Holds information needed to read a variation entry from a database. Access methods are defined for each known database type.

Variation entries are read from the database using the defined database access function, which is usually a static function within ajvardb.c

This should be a static data object but is needed for the definition of AjPVarin.

Alias name(s)

Name
AjSVarAccess
AjOVarAccess

Attributes

Name	Type	Description
Name	const char*	Access method name used in emboss.default
Access	AjBool function	Access function
AccessFree	AjBool function	Access cleanup function
Qlink	const char*	Supported query link operators
Desc	const char*	Description
Alias	AjBool	Alias for another name
Entry	AjBool	Supports retrieval of single entries
Query	AjBool	Supports retrieval of selected entries
All	AjBool	Supports retrieval of all entries
Chunked	AjBool	Supports retrieval of entries in chunks
Padding	AjBool	Padding to alignment boundary