File Formats - SeqAn API Documentation

# Group File Formats
Tags for identifying file formats.

## Grouped Tags Overview

- `Bam`
  Identify the BAM format.
- `typedef Tag<Bpseq_> Bpseq;`
  Bpseq format for RNA structures (*.bpseq).
- `typedef Tag<Connect_> Connect;`
  Connect format for RNA structures (*.ct).
- `typedef Tag<DotBracket_> DotBracket;`
  Dot Bracket format for RNA structures (*.dbn).
- `typedef Tag<Ebpseq_> Ebpseq;`
  Extended bpseq format for RNA structures (*.ebpseq).
- `typedef Tag<TagGff_> Gff;`
  Tag for selecting the GFF format.
- `typedef Tag<TagGtf_> Gtf;`
  Tag for selecting the GTF format.
- `typedef Tag<RnaStruct_> RnaStruct;`
  General RNA structure file type. The concrete type is defined by the file name suffix.
- `Sam`
  Identify the SAM format.
- `SimpleIntervals`
  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;`
  Stockholm format for RNA structures (*.sth).
- `typedef Tag<Ucsc_<UcscKnownGene_> > const Ucsc;`
  UCSC Genome browser annotation file (aka knownGene format).
- `typedef Tag<Ucsc_<UcscIsoforms_> > const UcscIsoforms;`
  UCSC Genome browser isoform file (aka knownIsoforms format).
- `typedef Tag<Vcf_> Vcf;`
  Variant callinf format file.
- `typedef Tag<Vienna_> Vienna;`
  Vienna format for RNA structures without pseudoknots (*.dbv).

## 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

#### Dox Sources

    /*!
     * @defgroup FileFormats File Formats
     *
     * @brief Tags for identifying file formats.
     *
     * @tag FileFormats#DotBracket
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Dot Bracket format for RNA structures (*.dbn).
     *
     * @signature typedef Tag<DotBracket_> DotBracket;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#Bpseq
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Bpseq format for RNA structures (*.bpseq).
     *
     * @signature typedef Tag<Bpseq_> Bpseq;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#Stockholm
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Stockholm format for RNA structures (*.sth).
     *
     * @signature typedef Tag<Stockholm_> Stockholm;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#RnaStruct
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief General RNA structure file type. The concrete type is defined by the
     *        file name suffix.
     *
     * @signature typedef Tag<RnaStruct_> RnaStruct;
     *
     * This tag is used as TSpec template parameter in @link FormattedFile @endlink.
     *
     * @see FileFormats#Connect
     * @see FileFormats#Stockholm
     * @see FileFormats#DotBracket
     * @see FileFormats#Vienna
     * @see FileFormats#Bpseq
     * @see FileFormats#Ebpseq
     *
     * @tag FileFormats#Ebpseq
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Extended bpseq format for RNA structures (*.ebpseq).
     *
     * @signature typedef Tag<Ebpseq_> Ebpseq;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#Vienna
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Vienna format for RNA structures without pseudoknots (*.dbv).
     *
     * @signature typedef Tag<Vienna_> Vienna;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#Connect
     *
     * @headerfile <seqan/rna_io.h>
     *
     * @brief Connect format for RNA structures (*.ct).
     *
     * @signature typedef Tag<Connect_> Connect;
     *
     * @see FileFormats#RnaStruct
     *
     * @tag FileFormats#Ucsc
     *
     * @headerfile <seqan/ucsc_io.h>
     *
     * @brief UCSC Genome browser annotation file (aka knownGene format).
     *
     * @signature typedef Tag<Ucsc_<UcscKnownGene_> > const Ucsc;
     *
     * @tag FileFormats#UcscIsoforms
     *
     * @headerfile <seqan/ucsc_io.h>
     *
     * @brief UCSC Genome browser isoform file (aka knownIsoforms format).
     *
     * @signature typedef Tag<Ucsc_<UcscIsoforms_> > const UcscIsoforms;
     *
     * @tag FileFormats#Bam
     *
     * @brief Identify the BAM format.
     *
     * @tag FileFormats#Sam
     *
     * @brief Identify the SAM format.
     *
     * @tag FileFormats#Gff
     *
     * @brief Tag for selecting the GFF format.
     *
     * @signature typedef Tag<TagGff_> Gff;
     *
     * Both the GFF and the GTF file format are represented by @link GffRecord
     * @endlink in SeqAn. Tags and functions in this group can be used for I/O of
     * both formats to and from @link GffRecord @endlink objects.
     *
     * @tag FileFormats#Gtf
     *
     * @brief Tag for selecting the GTF format.
     *
     * @signature typedef Tag<TagGtf_> Gtf;
     *
     * @tag FileFormats#Vcf
     *
     * @headerfile <seqan/vcf_io.h>
     *
     * @brief Variant callinf format file.
     *
     * @signature typedef Tag<Vcf_> Vcf;
     *
     * @tag FileFormats#SimpleIntervals
     *
     * @headerfile <seqan/simple_intervals_io.h>
     *
     * @brief Tag for the simple .intervals file format. The file contains format in
     *        the format <tt>CHR:POS</tt> or <tt>CHR:BEGIN-END</tt> in 1-based
     *        coordinates.
     */