#include <find_shared.hpp>

Inheritance diagram for vdj_pipe::Find_shared:

Collaboration diagram for vdj_pipe::Find_shared:

[legend]

Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"output sequence reads present in multiple sets") Find_shared(Vm_access_single const &vma

void	run ()

void	finish ()

void	summary (std::ostream &os) const

Public Member Functions inherited from vdj_pipe::detail::Step_base_single
void	reset_access (Value_ids_single const &ids)

Public Member Functions inherited from vdj_pipe::detail::Step_base
char	delimiter () const

	Step_base (boost::property_tree::ptree const &pt, Pipe_environment const &pe)

void	summary (std::ostream &) const

Public Attributes
boost::property_tree::ptree const &	pt

boost::property_tree::ptree const Pipe_environment &	pe

Private Types
typedef detail::Queable_ofstream_types::value_type	value_type

typedef detail::Queable_ofstream_types::val_vector	val_vector

typedef detail::Queable_ofstream_types::val_ref_vector	val_ref_vector

typedef detail::Id_bimap< Mapped_id, val_vector >	val_map_t

typedef std::vector< unsigned >	counts_v

typedef std::vector< counts_v >	hist_array_t

typedef boost::multi_array< unsigned, 2 >	xstats

Private Member Functions
void	write_sharing_matrix (std::ostream &os, counts_v const &cv, xstats const &xs, std::vector< Mapped_id > const &sorted_vi) const

void	write_summary (std::ostream &os, counts_v const &uc, counts_v const &guc, std::vector< Mapped_id > const &sn) const

void	write_redundancy (std::ostream &os, hist_array_t const &ha, std::vector< Mapped_id > const &sorted_vi) const

void	write_redundancy_summ (std::ostream &os, hist_array_t const &ha, std::vector< Mapped_id > const &sorted_vi) const

void	group_stats ()

void	bulk_stats ()

std::vector< Mapped_id >	sorted_ids () const

void	init_stream (boost::scoped_ptr< File_ostream > &, Variable_path const &, const compression::Compression, const format::Format) const

Private Attributes
Get_match_length	gml_

std::size_t	min_duplicates_

std::size_t	n_unique_

bool	trim_

bool	reverse_

bool	consensus_trim_

val_map_t	vm_

boost::shared_ptr< Read_ginfo_store >	rgs_

boost::shared_ptr< Seq_store >	ss_

counts_v	cv_

std::size_t	unique_count_

std::string	redund_hist_

std::string	summ_

value_type	unset_val_

Variable_path	g_unique_

Variable_path	g_dups_

Variable_path	unique_

Variable_path	dups_

std::vector< Val_id >	ids_

Additional Inherited Members
Public Types inherited from vdj_pipe::detail::Step_base_single
typedef Vm_access_single	vma_type

Public Types inherited from vdj_pipe::detail::Step_base
typedef Seq_record::sequence	seq_type

typedef Qual_record::quality	qual_type

Protected Member Functions inherited from vdj_pipe::detail::Step_base_single
	Step_base_single (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment const &pe)

Protected Attributes inherited from vdj_pipe::detail::Step_base_single
Vm_access_single	vma_

Member Typedef Documentation

typedef std::vector<unsigned> vdj_pipe::Find_shared::counts_v

private

typedef std::vector<counts_v> vdj_pipe::Find_shared::hist_array_t

private

typedef detail::Id_bimap<Mapped_id, val_vector> vdj_pipe::Find_shared::val_map_t

private

typedef detail::Queable_ofstream_types::val_ref_vector vdj_pipe::Find_shared::val_ref_vector

private

typedef detail::Queable_ofstream_types::val_vector vdj_pipe::Find_shared::val_vector

private

typedef detail::Queable_ofstream_types::value_type vdj_pipe::Find_shared::value_type

private

typedef boost::multi_array<unsigned, 2> vdj_pipe::Find_shared::xstats

private

Member Function Documentation

void vdj_pipe::Find_shared::bulk_stats ( )

private

void vdj_pipe::Find_shared::finish ( )

void vdj_pipe::Find_shared::group_stats ( )

private

void vdj_pipe::Find_shared::init_stream	(	boost::scoped_ptr< File_ostream > &	fos,
		Variable_path const &	vp,
		const compression::Compression	compr,
		const format::Format	fmt
	)		const

private

void vdj_pipe::Find_shared::run ( )

std::vector< Mapped_id > vdj_pipe::Find_shared::sorted_ids ( ) const

private

void vdj_pipe::Find_shared::summary ( std::ostream & os ) const

vdj_pipe::Find_shared::VDJ_PIPE_STATIC_STRING_METHOD	(	comment	,
		"output sequence reads present in multiple sets"
	)		const

void vdj_pipe::Find_shared::write_redundancy	(	std::ostream &	os,
		hist_array_t const &	ha,
		std::vector< Mapped_id > const &	sorted_vi
	)		const

private

void vdj_pipe::Find_shared::write_redundancy_summ	(	std::ostream &	os,
		hist_array_t const &	ha,
		std::vector< Mapped_id > const &	sorted_vi
	)		const

private

void vdj_pipe::Find_shared::write_sharing_matrix	(	std::ostream &	os,
		counts_v const &	cv,
		xstats const &	xs,
		std::vector< Mapped_id > const &	sorted_vi
	)		const

private

void vdj_pipe::Find_shared::write_summary	(	std::ostream &	os,
		counts_v const &	uc,
		counts_v const &	guc,
		std::vector< Mapped_id > const &	sn
	)		const

private

Member Data Documentation

bool vdj_pipe::Find_shared::consensus_trim_

private

counts_v vdj_pipe::Find_shared::cv_

private

Variable_path vdj_pipe::Find_shared::dups_

private

Variable_path vdj_pipe::Find_shared::g_dups_

private

Variable_path vdj_pipe::Find_shared::g_unique_

private

Get_match_length vdj_pipe::Find_shared::gml_

private

std::vector<Val_id> vdj_pipe::Find_shared::ids_

private

std::size_t vdj_pipe::Find_shared::min_duplicates_

private

std::size_t vdj_pipe::Find_shared::n_unique_

private

number of unique sequences not shared between groups

boost::property_tree::ptree const Pipe_environment& vdj_pipe::Find_shared::pe

boost::property_tree::ptree const& vdj_pipe::Find_shared::pt

std::string vdj_pipe::Find_shared::redund_hist_

private

bool vdj_pipe::Find_shared::reverse_

private

boost::shared_ptr<Read_ginfo_store> vdj_pipe::Find_shared::rgs_

private

boost::shared_ptr<Seq_store> vdj_pipe::Find_shared::ss_

private

std::string vdj_pipe::Find_shared::summ_

private

bool vdj_pipe::Find_shared::trim_

private

Variable_path vdj_pipe::Find_shared::unique_

private

std::size_t vdj_pipe::Find_shared::unique_count_

private

value_type vdj_pipe::Find_shared::unset_val_

private

val_map_t vdj_pipe::Find_shared::vm_

private

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

include/vdj_pipe/step/find_shared.hpp
lib/find_shared.cpp

Public Member Functions

Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Member Function Documentation

Member Data Documentation