vdj_pipe::input_detail Namespace Reference

Typedefs
typedef Seq_file_entry::map_t	val_map_t
typedef val_map_t::value_type	val_pair_t
typedef std::vector< val_map_t >	vvmap_t
typedef std::map< Val_id, int >	type_map_t

Functions
	VDJ_PIPE_KEYWORD_STRUCT (input_kwds,(forward_seq)(reverse_seq)(forward_mid)(reverse_mid)(forward_qual)(reverse_qual))
val_map_t	prepare_values (bpt::ptree const &pt, Value_map &vm)
void	harmonize_variables_1 (val_map_t &entry_vars, type_map_t &curr_types, type_map_t &change_to, std::set< Val_id > const &ign, Value_map const &vm)
void	harmonize_variables_2 (val_map_t &entry_vars, type_map_t const &change_to, Value_map const &vm)
void	harmonize_variables (vvmap_t &vvm, Value_map const &vm)

Typedef Documentation

typedef std::map<Val_id,int> vdj_pipe::input_detail::type_map_t

typedef Seq_file_entry::map_t vdj_pipe::input_detail::val_map_t

typedef val_map_t::value_type vdj_pipe::input_detail::val_pair_t

typedef std::vector<val_map_t> vdj_pipe::input_detail::vvmap_t

Function Documentation

void vdj_pipe::input_detail::harmonize_variables	(	vvmap_t &	vvm,
		Value_map const &	vm
	)

Make sure all required (non-ignorable) variables are present in all input entries. Make sure that all variables have same type

void vdj_pipe::input_detail::harmonize_variables_1	(	val_map_t &	entry_vars,
		type_map_t &	curr_types,
		type_map_t &	change_to,
		std::set< Val_id > const &	ign,
		Value_map const &	vm
	)

Exceptions

if	variable is present in curr_types, but neither in entry_vars nor

void vdj_pipe::input_detail::harmonize_variables_2	(	val_map_t &	entry_vars,
		type_map_t const &	change_to,
		Value_map const &	vm
	)

val_map_t vdj_pipe::input_detail::prepare_values	(	bpt::ptree const &	pt,
		Value_map &	vm
	)

vdj_pipe::input_detail::VDJ_PIPE_KEYWORD_STRUCT	(	input_kwds	,
		(forward_seq)(reverse_seq)(forward_mid)(reverse_mid)(forward_qual)(reverse_qual)
	)