btllib::SeqReader Class Reference

#include <seq_reader.hpp>

Classes
struct	Flag
struct	Record

Public Types
enum	Format {   UNDETERMINED, FASTA, FASTQ, SAM,   INVALID }

Public Member Functions
	SeqReader (const std::string &source_path, unsigned flags, unsigned threads=3)
	SeqReader (const SeqReader &)=delete
	SeqReader (SeqReader &&)=delete
SeqReader &	operator= (const SeqReader &)=delete
SeqReader &	operator= (SeqReader &&)=delete
void	close () noexcept
bool	fold_case () const
bool	trim_masked () const
bool	short_mode () const
bool	long_mode () const
Format	get_format () const
Record	read ()
OrderQueueMPMC< Record >::Block	read_block ()
RecordIterator	begin ()
RecordIterator	end ()
size_t	get_buffer_size () const
size_t	get_block_size () const

Static Public Attributes
static const size_t	MAX_SIMULTANEOUS_SEQREADERS = 256
static const size_t	SHORT_MODE_BUFFER_SIZE = 32
static const size_t	SHORT_MODE_BLOCK_SIZE = 32
static const size_t	LONG_MODE_BUFFER_SIZE = 4
static const size_t	LONG_MODE_BLOCK_SIZE = 1
static const size_t	FORMAT_BUFFER_SIZE = 16384

Friends
class	SeqReaderFastaModule
class	SeqReaderMultilineFastaModule
class	SeqReaderFastqModule
class	SeqReaderMultilineFastqModule
class	SeqReaderSamModule
std::ostream &	operator<< (std::ostream &os, const Format f)

Detailed Description

Read a FASTA, FASTQ or SAM file. When reading SAM files, samtools fastq is used to convert from the SAM format to the FASTQ format. Capable of reading gzip (.gz), bzip2 (.bz2), xz (.xz), zip (.zip), 7zip (.7z), lrzip (.lrz), BAM (.bam) and CRAM (.cram), and URL (http://, https://, ftp://) files. Threadsafe.

Examples:

seq_reader.cpp.

Constructor & Destructor Documentation

btllib::SeqReader::SeqReader	(	const std::string &	source_path,
		unsigned	flags,
		unsigned	threads = 3
	)

Construct a SeqReader to read sequences from a given path.

Parameters

source_path	Filepath to read from. Pass "-" to read from stdin.
flags	Modifier flags. Specifiying either short or long mode flag is mandatory; other flags are optional.
threads	Maximum number of helper threads to use. Must be at least 1.

Member Function Documentation

RecordIterator btllib::SeqReader::begin ( )

inline

For range-based for loop only.

Record btllib::SeqReader::read

(

)

Obtain next record.

OrderQueueMPMC<Record>::Block btllib::SeqReader::read_block

(

)

Obtain a whole block of records.

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

• include/btllib/seq_reader.hpp