Data structure for storing BED records.
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<Bed5> has members variables for the first 5 columns of a BED file. The remaining data is stored as the CharString member variable data.
Include Headers
The specialization to use.
Default: Bed12
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. When loading without using a BedIOContext, the rID field remains set to INVALID_REFID, otherwise the field is set to a different value.
Note that while the BED file format is 1-based, the coordinates in the BedRecord are 0-based.
Bed3 BedRecordBedRecord with 3 fields.
Data Members
beginPositionBegin position on the reference.
dataAny data after the last position.
endPositionEnd position on the reference.
INVALID_POSConstant for invalid positions.
INVALID_REFIDConstant for invalid references.
refName of the interval's reference (CharString).
rIDNumeric id of the interval's reference (__int32, defaults to INVALID_REFID).
Member Functions
clearReset BED record to state after default initialization.
readRecordRead a record from a BedStream
writeRecordWrite a record to a BedStream
SeqAn - Sequence Analysis Library -

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