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

SeqWriter()

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

write()

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