Group File Formats
Tags for identifying file formats.

Grouped Tags Overview

Grouped Tags Detail

Bam

Identify the BAM format.

typedef Tag<Bpseq_> Bpseq;

Defined in
<seqan/rna_io.h>
Bpseq format for RNA structures (*.bpseq).
See Also
RnaStruct

typedef Tag<Connect_> Connect;

Defined in
<seqan/rna_io.h>
Connect format for RNA structures (*.ct).
See Also
RnaStruct

typedef Tag<DotBracket_> DotBracket;

Defined in
<seqan/rna_io.h>
Dot Bracket format for RNA structures (*.dbn).
See Also
RnaStruct

typedef Tag<Ebpseq_> Ebpseq;

Defined in
<seqan/rna_io.h>
Extended bpseq format for RNA structures (*.ebpseq).
See Also
RnaStruct

typedef Tag<TagGff_> Gff;

Tag for selecting the GFF format.

Both the GFF and the GTF file format are represented by GffRecord in SeqAn. Tags and functions in this group can be used for I/O of both formats to and from GffRecord objects.

typedef Tag<TagGtf_> Gtf;

Tag for selecting the GTF format.

typedef Tag<RnaStruct_> RnaStruct;

Defined in
<seqan/rna_io.h>
General RNA structure file type. The concrete type is defined by the file name suffix.
See Also
Bpseq
Connect
DotBracket
Ebpseq
Stockholm
Vienna

This tag is used as TSpec template parameter in FormattedFile.

Sam

Identify the SAM format.

SimpleIntervals

Defined in
<seqan/simple_intervals_io.h>
Tag for the simple .intervals file format. The file contains format in the format CHR:POS or CHR:BEGIN-END in 1-based coordinates.

typedef Tag<Stockholm_> Stockholm;

Defined in
<seqan/rna_io.h>
Stockholm format for RNA structures (*.sth).
See Also
RnaStruct

typedef Tag<Ucsc_<UcscKnownGene_> > const Ucsc;

Defined in
<seqan/ucsc_io.h>
UCSC Genome browser annotation file (aka knownGene format).

typedef Tag<Ucsc_<UcscIsoforms_> > const UcscIsoforms;

Defined in
<seqan/ucsc_io.h>
UCSC Genome browser isoform file (aka knownIsoforms format).

typedef Tag<Vcf_> Vcf;

Defined in
<seqan/vcf_io.h>
Variant callinf format file.

typedef Tag<Vienna_> Vienna;

Defined in
<seqan/rna_io.h>
Vienna format for RNA structures without pseudoknots (*.dbv).
See Also
RnaStruct