Group FASTA/FASTQ I/O

Functions for FASTA and FASTQ I/O.

/*!
 * @defgroup FastaFastqIO FASTA/FASTQ I/O
 * 
 * @brief Functions for FASTA and FASTQ I/O.
 * 
 * These functions are very low-level. Consider using @link SequenceStream
 * @endlink for an easier to use API.
 * 
 * @fn FastaFastqIO#readRecord
 * 
 * @headerfile <seqan/seq_io.h>
 * 
 * @brief Read one FASTA or FASTQ record.
 * 
 * @signature int readRecord(id, seq[, quals], stream, tag);
 * 
 * @param[in,out] stream The @link StreamConcept @endlink to read from.
 * @param[in] id @link SequenceConcept @endlink to read identifier into.
 * @param[in] seq @link SequenceConcept @endlink to read sequence into.
 * @param[in] quals @link SequenceConcept @endlink to read qualities into.
 * @param[in] tag The format selector. Types: <tt>Fasta</tt>, <tt>Fastq</tt>
 * 
 * @return int 0 on success, non-0 value on errors.
 * 
 * @fn FastaFastqIO#read2
 * 
 * @headerfile <seqan/seq_io.h>
 * 
 * @brief Read a whole FASTA or FASTQ file into StringSet objects.
 * 
 * @signature int read2(ids, seqs[, quals], reader, tag);
 * 
 * @param[in,out] stream The @link StreamConcept @endlink to read from.
 * @param[in] ids The @link StringSet @endlink to read the ids into.
 * @param[in] seqs The @link StringSet @endlink to read the sequences into.
 * @param[in] quals The @link StringSet @endlink to read the ASCII qualities
 *                  into.
 * @param[in] tags The format selector. Types: <tt>Fasta</tt>, <tt>Fastq</tt>
 * 
 * @return int 0 on success, non-0 value on errors.
 * 
 * @fn FastaFastqIO#writeRecord
 * 
 * @headerfile <seqan/seq_io.h>
 * 
 * @brief Write one FASTA or FASTQ record.
 * 
 * @signature int writeRecord(stream, id, seq[, quals], tag[, options]);
 * 
 * @param[in,out] stream The stream to write to. Type: @link StreamConcept
 *                       @endlink
 * @param[in] id ID/Meta information line to write out. Types: @link
 *               SequenceConcept @endlink
 * @param[in] seq Sequence to write out. Type: @link SequenceConcept @endlink
 * @param[in] quals ASCII quality characters to write out. Types: @link
 *                  SequenceConcept @endlink
 * @param[in] tag The format selector. Types: <tt>Fasta</tt>, <tt>Fastq</tt>
 * @param[in] options if not supplied, defaults are chosen. Types: @link
 *                    SequenceOutputOptions @endlink
 * 
 * @return int 0 on success, non-0 value on errors.
 * 
 * @fn FastaFastqIO#write2
 * 
 * @headerfile <seqan/seq_io.h>
 * 
 * @brief Write FASTA or FASTQ records.
 * 
 * @signature int write2(stream, ids, seqs[, quals], tag[, options]);
 * 
 * @param[in,out] stream The stream to write to. Types: @link StreamConcept
 *                       @endlink
 * @param[in] ids IDs/Metainformation strings to write out. Type: @link
 *                StringSet @endlink
 * @param[in] seqs Sequences to write out. Type: @link StringSet @endlink
 * @param[in] quals ASCII quality characters to write out. Type: @link StringSet
 *                  @endlink
 * @param[in] tag The format selector. Types: <tt>Fasta</tt>, <tt>Fastq</tt>
 * @param[in] options if not supplied defaults are chosen. Type: @link
 *                    SequenceOutputOptions @endlink
 * 
 * @return int 0 on success, non-0 value on errors.
 */