vdj_pipe::Group_unique Class Reference

#include <find_shared_impl.hpp>

Collaboration diagram for vdj_pipe::Group_unique:

Public Member Functions
	Group_unique (Seq_store &ss, Read_ginfo_store const &rgs, const unsigned n_mids, const Mapped_id mid, Get_match_length const &gml)
unsigned	n_reads () const
void	write_group_unique (File_ostream &fos, const unsigned min_duplicates, const bool consensus_trim, const std::string group_name) const
void	write_unique (File_ostream &fos, const unsigned min_duplicates) const
void	write_redundancy (std::ostream &os, const char delim) const
unsigned	find_shared (xstats &xs1, xstats &xs2)
void	group_redundancy_histogram (xstats &h) const
void	redundancy_histogram (xstats &h) const

Private Types
typedef boost::container::flat_map< Seq_id, Sequence_gstats >	seq_map
typedef seq_map::value_type	pair
typedef std::vector< unsigned >	xstats

Private Member Functions
void	store_stats (const unsigned seq_len, const unsigned match_pos, const unsigned match_len, super_seq const &super, Group_count const &gc)
bool	check_duplicates (std::string const &seq, Group_count const &gc)
bool	find_shared (const Seq_id sid, Group_count const &gc)
Read_id	find_id (const Seq_id sid) const
bool	is_only_group (const Seq_id sid, const Mapped_id mid) const
void	find_duplicates (const Seq_id sid, Group_count const &gc)

Private Attributes
gdst::Gdst	st_
seq_map	m_
Seq_store const &	ss_
Read_ginfo_store const &	rgs_
unsigned	n_mids_
Mapped_id	mid_
Get_match_length const &	gml_

Member Typedef Documentation

typedef seq_map::value_type vdj_pipe::Group_unique::pair

private

typedef boost::container::flat_map<Seq_id, Sequence_gstats> vdj_pipe::Group_unique::seq_map

private

typedef std::vector<unsigned> vdj_pipe::Group_unique::xstats

private

Constructor & Destructor Documentation

vdj_pipe::Group_unique::Group_unique ( Seq_store &  ss, Read_ginfo_store const &  rgs, const unsigned  n_mids, const Mapped_id  mid, Get_match_length const &  gml  )

inline

Member Function Documentation

bool vdj_pipe::Group_unique::check_duplicates ( std::string const &  seq, Group_count const &  gc  )

inlineprivate

Parameters

seq	sequence without ambiguous nucleotides
gc

Returns

true if sequence has a match in stored sequences

void vdj_pipe::Group_unique::find_duplicates ( const Seq_id  sid, Group_count const &  gc  )

inlineprivate

Read_id vdj_pipe::Group_unique::find_id ( const Seq_id  sid ) const

inlineprivate

unsigned vdj_pipe::Group_unique::find_shared ( xstats &  xs1, xstats &  xs2  )

inline

bool vdj_pipe::Group_unique::find_shared ( const Seq_id  sid, Group_count const &  gc  )

inlineprivate

Parameters

sid
gc

void vdj_pipe::Group_unique::group_redundancy_histogram ( xstats &  h ) const

inline

bool vdj_pipe::Group_unique::is_only_group ( const Seq_id  sid, const Mapped_id  mid  ) const

inlineprivate

unsigned vdj_pipe::Group_unique::n_reads ( ) const

inline

void vdj_pipe::Group_unique::redundancy_histogram ( xstats &  h ) const

inline

void vdj_pipe::Group_unique::store_stats ( const unsigned  seq_len, const unsigned  match_pos, const unsigned  match_len, super_seq const &  super, Group_count const &  gc  )

inlineprivate

void vdj_pipe::Group_unique::write_group_unique ( File_ostream &  fos, const unsigned  min_duplicates, const bool  consensus_trim, const std::string  group_name  ) const

inline

void vdj_pipe::Group_unique::write_redundancy ( std::ostream &  os, const char  delim  ) const

inline

void vdj_pipe::Group_unique::write_unique ( File_ostream &  fos, const unsigned  min_duplicates  ) const

inline

Member Data Documentation

Get_match_length const& vdj_pipe::Group_unique::gml_

private

seq_map vdj_pipe::Group_unique::m_

private

Mapped_id vdj_pipe::Group_unique::mid_

private

unsigned vdj_pipe::Group_unique::n_mids_

private

Read_ginfo_store const& vdj_pipe::Group_unique::rgs_

private

Seq_store const& vdj_pipe::Group_unique::ss_

private

gdst::Gdst vdj_pipe::Group_unique::st_

private

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

• lib/find_shared_impl.hpp