Inheritance diagram for vdj_pipe::Homopolymer_filter:

Collaboration diagram for vdj_pipe::Homopolymer_filter:

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Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"discard reads that contain a homopolymer longer than minimal length") Homopolymer_filter(Vm_access_single const &vma

void	run ()

void	finish ()

Public Member Functions inherited from vdj_pipe::detail::Filter_base
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

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::Filter_base
	VDJ_PIPE_KEYWORD_STRUCT (kwds,(passed_name))

	Filter_base (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)

void	pass (const bool b)

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::Filter_base
std::size_t	nf_

Val_id	pass_id_

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

Member Function Documentation

void vdj_pipe::Homopolymer_filter::finish ( )

inline

void vdj_pipe::Homopolymer_filter::run ( )

vdj_pipe::Homopolymer_filter::VDJ_PIPE_STATIC_STRING_METHOD	(	comment	,
		"discard reads that contain a homopolymer longer than minimal length"
	)		const

Member Data Documentation

unsigned vdj_pipe::Homopolymer_filter::min_

private

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

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

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