btllib::SeqReader Class Reference

#include <seq_reader.hpp>

Classes
struct	read_fasta_buffer
struct	read_fasta_file
struct	read_fasta_transition
struct	read_fastq_buffer
struct	read_fastq_file
struct	read_fastq_transition
struct	read_gfa2_buffer
struct	read_gfa2_file
struct	read_gfa2_transition
struct	read_sam_buffer
struct	read_sam_file
struct	read_sam_transition
struct	Record

Public Types
enum	Flag { FOLD_CASE = 0, NO_FOLD_CASE = 1, NO_TRIM_MASKED = 0, TRIM_MASKED = 2 }
enum	Format {   UNDETERMINED, FASTA, FASTQ, SAM,   GFA2, INVALID }

Public Member Functions
	SeqReader (const std::string &source_path, int flags=0)
void	close () noexcept
bool	flagFoldCase () const
bool	flagTrimMasked () const
Format	get_format () const
Record	read ()

Detailed Description

Read a FASTA, FASTQ, SAM, or GFA2 file. Threadsafe.

Member Enumeration Documentation

Flag

enum btllib::SeqReader::Flag

Enumerator
FOLD_CASE	Fold lower-case characters to upper-case.
NO_TRIM_MASKED	Trim masked (lower case) characters from the ends of sequences.

Member Function Documentation

read()

SeqReader::Record btllib::SeqReader::read ( )

inline

Read operator.

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

• include/btllib/seq_reader.hpp