Class BedRecord
Data 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

Member Functions Inherited From AssignableConcept

Interface Function Overview

Interface Functions Inherited From AssignableConcept

Member Variable Overview

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.


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



Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Functions Detail

void clear(record);

Reset BED record to state after default initialization.


record BedRecord to reset.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Member Variables Detail

int32_t BedRecord::beginPos

Begin position on the reference.

CharString BedRecord::data

Any data after the last position.

int32_t BedRecord::endPos

End position on the reference.

int32_t BedRecord::INVALID_POS

Constant for invalid positions.

int32_t BedRecord::INVALID_REFID

Constant for invalid references.

CharString BedRecord::ref

Name of the interval's reference name.

int32_t BedRecord::rID

Numeric id of the interval's reference (int32_t, defaults to INVALID_REFID).