Class
BedRecordData structure for storing BED records.
Implements | FormattedFileRecordConcept |
---|---|
All Subcl's | Bed12Record, Bed3Record, Bed4Record, Bed5Record, Bed6Record |
All Impl'd | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept |
Defined in | <seqan/bed_io.h> |
Signature |
template <typename TSpec>
class BedRecord;
|
Template Parameters
TSpec |
The specialization to use. Default: Bed12. |
---|
Member Function Overview
-
BedRecord::BedRecord();
Constructor.
Member Functions Inherited From AssignableConcept
Interface Function Overview
-
void clear(record);
Reset BED record to state after default initialization.
Interface Functions Inherited From AssignableConcept
Member Variable Overview
-
__int32 BedRecord::beginPosition
Begin position on the reference. -
CharString BedRecord::data
Any data after the last position. -
__int32 BedRecord::endPosition
End position on the reference. -
__int32 BedRecord::INVALID_POS
Constant for invalid positions. -
__int32 BedRecord::INVALID_REFID
Constant for invalid references. -
CharString BedRecord::ref
Name of the interval's reference name. -
__int32 BedRecord::rID
Numeric id of the interval's reference (__int32, defaults to INVALID_REFID).
Detailed Description
BED files allow the easy representation of intervals on the genome. Originally, they were designed for tracks in the UCSC genome browser. The original format has 12 columns but often variants using fewer columns with interpreted data are used and the rest is kept as application dependent data.
The BedRecord class allows for storing BED records. The various subclasses provide access to 3, 4, 5, 6, or 12 fields of the BED format. For example, a BedRecord<Bed>> has members variables for the first 5 columns of a BED file. The remaining data is stored as the CharString member variable data.
Remarks
The ref field is the name of the reference as loaded from the BED file. The rID field can be used to store a numeric reference id.
Note that while the BED file format is 1-based, the coordinates in the BedRecord are 0-based.
Member Functions Detail
BedRecord::BedRecord();
Interface Functions Detail
void clear(record);
Parameters
record
|
BedRecord to reset. |
---|