7 #ifndef SEQUENCE_FILE_ENTRY_HPP_ 8 #define SEQUENCE_FILE_ENTRY_HPP_ 11 #include "boost/property_tree/ptree_fwd.hpp" 29 typedef std::map<Val_id, value_variant>
map_t;
38 const_iterator
begin()
const {
return map_.begin();}
39 const_iterator
end()
const {
return map_.end();}
46 return get_str(seq_,
"sequence");
50 return get_str(qual_,
"quality");
54 return get_str(seq_rev_,
"reverse sequence");
58 return get_str(qual_rev_,
"reverse quality");
61 std::string
const&
mid()
const {
62 return get_str(mid_,
"MID");
66 return get_str(mid_rev_,
"reverse MID");
81 std::string
const&
get_str(
const Val_id
id, std::string
const& msg)
const {
82 const const_iterator i = map_.find(
id);
83 if( i == map_.end() ) BOOST_THROW_EXCEPTION(
87 return boost::get<std::string>(i->second);
std::string const & mid_rev() const
Definition: sequence_file_entry.hpp:65
map_t map_
Definition: sequence_file_entry.hpp:77
const_iterator begin() const
Definition: sequence_file_entry.hpp:38
map_t::value_type value_type
Definition: sequence_file_entry.hpp:32
map_t::const_iterator iterator
Definition: sequence_file_entry.hpp:30
qual_type qt_
Definition: sequence_file_entry.hpp:70
qual_type
Definition: sequence_file_entry.hpp:27
std::string const & quality() const
Definition: sequence_file_entry.hpp:49
bool is_paired() const
Definition: sequence_file_entry.hpp:40
bool has_qual_file() const
Definition: sequence_file_entry.hpp:43
std::map< Val_id, value_variant > map_t
Definition: sequence_file_entry.hpp:29
std::string const & sequence() const
Definition: sequence_file_entry.hpp:45
Val_id qual_
Definition: sequence_file_entry.hpp:72
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Qual_record::quality qual
Definition: match_element_run.cpp:26
Val_id seq_rev_
Definition: sequence_file_entry.hpp:73
std::string const & mid() const
Definition: sequence_file_entry.hpp:61
std::string const & get_str(const Val_id id, std::string const &msg) const
Definition: sequence_file_entry.hpp:81
#define VDJ_PIPE_DECL
Definition: config.hpp:23
Val_id qual_rev_
Definition: sequence_file_entry.hpp:74
Val_id seq_
Definition: sequence_file_entry.hpp:71
Definition: sequence_file_entry.hpp:26
std::string const & seq_rev() const
Definition: sequence_file_entry.hpp:53
Val_id mid_rev_
Definition: sequence_file_entry.hpp:76
const_iterator end() const
Definition: sequence_file_entry.hpp:39
void store_values(Seq_file_entry const &sfe, Value_map &vm)
Definition: sequence_file_entry.cpp:119
Definition: exception.hpp:23
boost::error_info< struct errinfo_message_, std::string > msg_t
Definition: exception.hpp:24
Definition: sequence_file_entry.hpp:34
bool has_emid() const
Definition: sequence_file_entry.hpp:41
bool has_quality() const
Definition: sequence_file_entry.hpp:42
Store values mapped against name strings and value IDs.
Definition: value_map.hpp:23
Definition: file_properties.hpp:20
map_t::const_iterator const_iterator
Definition: sequence_file_entry.hpp:31
Val_id mid_
Definition: sequence_file_entry.hpp:75
std::string const & qual_rev() const
Definition: sequence_file_entry.hpp:57