#include <seq_reader.hpp>

Classes
struct	Flag

struct	Record

Public Types
enum class	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

◆ SeqReader()

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

◆ begin()

RecordIterator btllib::SeqReader::begin ( )

inline

For range-based for loop only.

◆ read()

Record btllib::SeqReader::read ( )

Obtain next record.

◆ read_block()

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

Obtain a whole block of records.

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

include/btllib/seq_reader.hpp

Classes

Public Types

Public Member Functions

Static Public Attributes