Class UcscRecord
Represent the information for one UCSC gene annotation record.

Implements FormattedFileRecordConcept
All Impl'd AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept
Defined in <seqan/ucsc_io.h>
Signature class UcscRecord;

Member Function Overview

Member Functions Inherited From AssignableConcept

Interface Function Overview

Interface Functions Inherited From AssignableConcept

Member Variable Overview

Detailed Description

The UCSC genome browser server allows the download of a set of the known genes and isoforms used in the browser. These files can be downloaded from the UCSC FTP's goldenPath folder, e.g. the one for hg19.

To load the annotations, you need to download both the knownGenes.txt.gz and the knownIsoforms.txt.gz files from the UCSC goldenPath database. These files can then be read record by record into a UcscRecord. This record type is capable of representing records from either file type.

Interface Functions Detail

void clear(record);

Clear UcscRecord.


record The UcscRecord to clear.

Clears all strings and resets it to default initialization state.

Data Races

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

Member Variables Detail

uint32_t UcscRecord::annotationBeginPos

Start of the annotation (0-based, defaults to -1).

CharString UcscRecord::annotationEndPos

End position of the annotation, defaults to -1.

int32_t UcscRecord::cdsBegin

Start of the coding region (0-based position, defaults to -1).

int32_t UcscRecord::cdsEnd

End of the coding region, defaults to -1.

CharString UcscRecord::contigName

Name of the contig of the genomic location.

CharString UcscRecord::exonBegin

Start of the exon (0-based position, defaults to -1).

CharString UcscRecord::exonEnds

End of the exon, defaults to -1.

CharString UcscRecord::proteinName

Name of the coded protein.

CharString UcscRecord::transName

Name of the transcript.