btllib::SeqWriter Class Reference

#include <seq_writer.hpp>

Public Types
enum	Format { FASTA, FASTQ }

Public Member Functions
	SeqWriter (const std::string &sink_path, Format format=FASTA, bool append=false)
void	close ()
void	write (const std::string &id, const std::string &comment, const std::string &seq, const std::string &qual="")

Detailed Description

Write FASTA or FASTQ sequences to a file. Capable of writing gzip (.gz), bzip2 (.bz2), xz (.xz), zip (.zip), 7zip (.7z), and lrzip (.lrz) files. Add the appropriate extension to the output filename to automatically compress. Threadsafe.

Examples:

seq_writer.cpp.

Constructor & Destructor Documentation

btllib::SeqWriter::SeqWriter	(	const std::string &	sink_path,
		Format	format = FASTA,
		bool	append = false
	)

Construct a SeqWriter to write sequences to a given path.

Parameters

source_path	Filepath to write to. Pass "-" to write to stdout.
format	Which format to write the output as.
append	Whether to append to the target file or write anew.

Member Function Documentation

void btllib::SeqWriter::write	(	const std::string &	id,
		const std::string &	comment,
		const std::string &	seq,
		const std::string &	qual = ""
	)

Write a sequence.

Parameters

id	Sequence ID or name.
comment	Optional comment after the ID/name.
seq	The sequence to write.
qual	Optional quality scores, mandatory if format is FASTQ.

Examples:

seq_writer.cpp.

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The documentation for this class was generated from the following file:

• include/btllib/seq_writer.hpp