ajassemdata

Enum AjEAssemSortOrder

Enumerated value(s)

Name
ajEAssemSortOrderUnknown	Unknown - default in SAM/BAM formats
ajEAssemSortOrderUnsorted	Unsorted - unsorted
ajEAssemSortOrderQueryname	Queryname - sorted by query/read names
ajEAssemSortOrderCoordinate	Coordinate - major sort key is the the reference/contig name, order defined by the order of

Enum AjEAssemPlatform

Enumerated value(s)

Name
ajEAssemPlatformUnknown	Unknown
ajEAssemPlatformCapillary	Capillary
ajEAssemPlatformLS454	LS 454
ajEAssemPlatformIllumina	Illumina
ajEAssemPlatformSolid	Solid
ajEAssemPlatformHelicos	Helicos
ajEAssemPlatformIontorrent	IonTorrent
ajEAssemPlatformPacbio	Pacific Biosciences

Data type AjPAssemRead

In some assemblies some reads can align to more than one contig or reference sequence, so current name of the data type is not perfect.

For storing read information as part of an assembly object. Current version of this data type is MIRA/SAM oriented, it needs to be improved to be a proper common data type, some of the current fields are used by MIRA MAF format only while few others are used by the SAM format only.

Alias name(s)

Name
AjSAssemRead
AjOAssemRead

Attributes

Name	Type	Description
Name	AjPStr	Name
Seq	AjPStr	Sequence
SeqQ	AjPStr	Sequence quality string
Template	AjPStr	Name of the DNA template a sequence comes from
File	AjPStr	Name of the sequencing file which contains raw data for this read
Technology	AjPStr	Sequencing technology
Cigar	AjPStr	CIGAR string
Tags	AjPList	List of AjPAssemTag objects
AlignmentBlocks	AjPList	Alignment blocks
Rnext	ajlong	Reference number of the mate/next fragment
Reference	ajlong	Reference sequence
Pnext	ajlong	Position of the mate/next fragment
Tlen	ajint	Observed template length
Flag	ajint	Flag
MapQ	ajint	Map quality
TemplateSizeMin	ajint	Minimum template size
TemplateSizeMax	ajint	Maximum template size
ClipLeft	ajint	Clip left
ClipRight	ajint	Clip right
VectorLeft	ajint	Clip left due to sequencing vector
VectorRight	ajint	Clip right due to sequencing vector
QualLeft	ajint	Clip left due to quality
QualRight	ajint	Clip right due to quality
x1	ajint	interval of the contig (1-based as in SAM and MAF)
y1	ajint	end of contig interval
x2	ajint	interval of the read
y2	ajint	end of read interval
Reversed	AjBool	true: has been reverse-complemented
Direction	char	Direction of the read with respect to the template
Padding	char[7]	Padding to alignment boundary

Data type AjPAssemContig

In mapping assemblies consensus sequence refers to the reference sequence.

Attributes

Name	Type	Description
Name	AjPStr	Name
Consensus	AjPStr	Consensus/reference sequence
ConsensusQ	AjPStr	Quality string for the consensus sequence
Tags	AjPList	Tags for the consensus sequence
Length	ajint	Length of the consensus sequence
Nreads	ajint	Number of reads
AssemblyID	AjPStr	Assembly ID
MD5	AjPStr	MD5 checksum of the consensus sequence in the uppercase, with gaps and spaces removed
Species	AjPStr	Species
URI	AjPStr	URI of the consensus sequences

Data type AjPAssemin

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

Alias name(s)

Name
AjSAssemin
AjOAssemin

Attributes

Name	Type	Description
Input	AjPTextin	General text input object
BamIdx	AjPBamIndex	BAM index
BamInput	AjBool	BAM file input
cbegin	ajint	Contig start position
cend	ajint	Contig end position
Loading	AjBool	True if data is now loading

Data type AjPAssem

Holds the assembly itself, plus associated information.

Alias name(s)

Name
AjSAssem
AjOAssem

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
BamHeader	AjPSeqBamHeader	BAM header
Contigs	AjPTable	Contigs table, storing contigs by name
ContigsIgnored	AjPTable	Contigs named as '*' because of missing header '

Attributes

Name	Type	Description
ContigsOrder	AjPList	Order of contigs in the assembly
ContigArray	AjPAssemContig*	Contigs array for fast access
Reads	AjPList	List of reads in the assembly
Readgroups	AjPTable	Table of read-groups in the assembly
rec	AjPAssemRead	Current/last read/alignment record read
Fpos	ajlong	File position
Format	AjEnum	Input format enum
Count	ajuint	Number of lines read (contigs in case of BAM)
Hasdata	AjBool	True when data has been loaded
SO	AjEAssemSortOrder	Reads sort order in the assembly

Data type AjPAssemload

Inherits an AjPAssem but allows more assembly data to be read from the same input by also inheriting the AjPVarin input object.

Alias name(s)

Name
AjSAssemload
AjOAssemload

Attributes

Name	Type	Description
Assem	AjPAssem	Current variation
Assemin	AjPAssemin	Assembly input for reading next
Count	ajuint	Count of terms so far
Loading	AjBool	True if data is now loading
Returned	AjBool	if true: Assembly 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 AjPAssemAccess

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

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

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

Alias name(s)

Name
AjSAssemAccess
AjOAssemAccess

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

Data type AjPAssemTag

SAM format also allows a set of predefined tags as well as it reserves lowercase tags for end users.

Attributes

Name	Type	Description
Name	AjPStr	Name
Comment	AjPStr	Tag comment in case of MAF, or tag value in case of SAM
x1	ajuint	X value
y1	ajuint	Y value
type	char	Value type: AcCsSiIfZHB
Padding	char[7]	Padding to alignment boundary

Data type AjPAssemReadalignmentblock

Attributes

Name	Type	Description
readStart	int	Read start
referenceStart	int	Reference start
length	int	alignment length

Data type AjPAssemReadgroup

Attributes

Name	Type	Description
ID	AjPStr	Read group identifier
CN	AjPStr	Name of the sequencing center producing the read
Desc	AjPStr	Description
Date	AjPStr	Date the run was produced
FlowOrder	AjPStr	The array of nucleotide bases that correspond to the nucleotides used for each flow of each record
KeySeq	AjPStr	The array of nucleotide bases that correspond to the key sequence of each read
Library	AjPStr	Library
Programs	AjPStr	Programs used for processing the read group
Unit	AjPStr	Platform unit (e.g. flowcell-barcode for Illumina)
Sample	AjPStr	Sample name, or pool name when a pool was sequenced
Isize	ajint	Predicted median insert size
Platform	AjEAssemPlatform	Instrument platform