Inheritance diagram for vdj_pipe::Ambiguous_window_filter:

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Collaboration diagram for vdj_pipe::Ambiguous_window_filter:

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Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"Truncate reads to bring number of ambiguous bases below maximum") VDJ_PIPE_STATIC_STRING_METHOD(description

Find read interval at least min_len nucleotides long that has at most max_ambiguous ambiguous nucleotides Discard reads where such interval cannot be found If min_len is require that the whole read contains at most max_ambiguous ambiguous nucleotides	Ambiguous_window_filter (Vm_access_single const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)

void	run ()

void	finish ()

Public Member Functions inherited from vdj_pipe::detail::Window_filter_base
void	summary (std::ostream &os) const

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
Find read interval at least min_len nucleotides long that has at most max_ambiguous ambiguous nucleotides Discard reads where such interval cannot be found If min_len is	zero

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

void	trim (sequence_interval const &si)

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::Window_filter_base
std::size_t	nt_

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_

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

Public Member Functions

Public Attributes