7 #ifndef PARSER_FASTA_HPP_ 8 #define PARSER_FASTA_HPP_ 26 <<
Err::msg_t(
"wrong file format for FASTA parser")
42 const boost::string_ref
get_id() {
return Parser_line::get_id(
'>');}
44 const boost::string_ref
get_defstr() {
return Parser_line::get_defstr(
'>');}
49 Parser_line::set_meta(sr,
'>');
Seq_record record
Definition: parser_fasta.hpp:18
Parser_fasta(File_input const &fi)
Definition: parser_fasta.hpp:21
format::Format format() const
Definition: file.hpp:75
sequence seq_
Definition: sequence_record.hpp:32
Compression
File compression types.
Definition: file_properties.hpp:19
boost::error_info< struct errinfo_int1_, int > int1_t
Definition: exception.hpp:28
void next_record()
Definition: parser_fasta.hpp:43
Definition: parser_line.hpp:26
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Parser_line(File_input const &fi)
Definition: parser_line.hpp:34
std::string const & path() const
Definition: file.hpp:74
Definition: sequence_record.hpp:28
record::sequence sequence
Definition: parser_fasta.hpp:19
record get_record()
Definition: parser_fasta.hpp:47
boost::error_info< struct errinfo_str1_, std::string > str1_t
Definition: exception.hpp:25
Definition: parser_fasta.hpp:16
const boost::string_ref get_defstr()
Definition: parser_fasta.hpp:44
std::string sequence
Definition: sequence_record.hpp:29
boost::error_info< struct errinfo_message_, std::string > msg_t
Definition: exception.hpp:24
std::string sanitize(const char c)
Definition: sanitize_string.cpp:53
sequence get_sequence()
Definition: parser_fasta.hpp:45
Basic line-based parser; use to derive other parsers.
Definition: parser_line.hpp:23
const boost::string_ref get_id()
Definition: parser_fasta.hpp:42
Parser_fasta(std::istream &is, const compression::Compression compr=compression::none)
Definition: parser_fasta.hpp:33
Definition: file_properties.hpp:20