btllib
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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

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.


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