Search Toolkit Book for NAdapterSearch::CPairedEndAdapterDetector

#include <algo/sequence/adapter_search.hpp>

Inheritance diagram for NAdapterSearch::CPairedEndAdapterDetector:

Collaboration diagram for NAdapterSearch::CPairedEndAdapterDetector:

Classes
class	CConsensusPattern
	CConsensusPattern calculates most frequent pattern from a set of (noisy) exemplars based on distribution of 10-mer frequencies at every position of the pattern. More...

Public Member Functions
	CPairedEndAdapterDetector (size_t max_len=100)

virtual void	AddExemplar (const char *seq, size_t len)
	Add examplar paired-end spot seq = fwd_read + rev_read; \|fwd_read\|=\|rev_read\|=len/2 Reads are in original orientation ->...<- (as in fastq-dump) More...

virtual string	InferAdapterSeq () const
	The returned string contains '-'-delimited pair of IUPAC strings for 5' and 3' adapter respectively. More...

Public Member Functions inherited from NAdapterSearch::IAdapterDetector
SParams &	SetParams ()

const SParams &	GetParams () const

virtual	~IAdapterDetector ()

Static Private Member Functions
static pair< size_t, size_t >	s_FindAdapterStartPos (const TWords &fwd_read, const TWords &rev_read)
	Given a paired-end read in consistent orientations with a fragment-overlap overlap, compute the putative positions of the adapter starts. More...

Private Attributes
CConsensusPattern	m_cons5

CConsensusPattern	m_cons3

Additional Inherited Members
Protected Attributes inherited from NAdapterSearch::IAdapterDetector
SParams	m_params

Detailed Description

Definition at line 198 of file adapter_search.hpp.

Constructor & Destructor Documentation

◆ CPairedEndAdapterDetector()

NAdapterSearch::CPairedEndAdapterDetector::CPairedEndAdapterDetector ( size_t max_len = 100 )

inline

Definition at line 250 of file adapter_search.hpp.

Member Function Documentation

◆ AddExemplar()

void NAdapterSearch::CPairedEndAdapterDetector::AddExemplar	(	const char *	seq,
		size_t	len
	)

virtual

Add examplar paired-end spot seq = fwd_read + rev_read; |fwd_read|=|rev_read|=len/2 Reads are in original orientation ->...<- (as in fastq-dump)

Implements NAdapterSearch::IAdapterDetector.

Definition at line 275 of file adapter_search.cpp.

References len, and NAdapterSearch::s_Translate().

◆ InferAdapterSeq()

virtual string NAdapterSearch::CPairedEndAdapterDetector::InferAdapterSeq ( ) const

inlinevirtual

The returned string contains '-'-delimited pair of IUPAC strings for 5' and 3' adapter respectively.

Implements NAdapterSearch::IAdapterDetector.

Definition at line 262 of file adapter_search.hpp.

References NAdapterSearch::CPairedEndAdapterDetector::CConsensusPattern::InferConsensus(), m_cons3, m_cons5, and NAdapterSearch::IAdapterDetector::m_params.

◆ s_FindAdapterStartPos()

pair< size_t, size_t > NAdapterSearch::CPairedEndAdapterDetector::s_FindAdapterStartPos	(	const TWords &	fwd_read,
		const TWords &	rev_read
	)

staticprivate

Given a paired-end read in consistent orientations with a fragment-overlap overlap, compute the putative positions of the adapter starts.

Definition at line 260 of file adapter_search.cpp.

Member Data Documentation

◆ m_cons3

CConsensusPattern NAdapterSearch::CPairedEndAdapterDetector::m_cons3

private

Definition at line 276 of file adapter_search.hpp.

Referenced by InferAdapterSeq().

◆ m_cons5

CConsensusPattern NAdapterSearch::CPairedEndAdapterDetector::m_cons5

private

Definition at line 275 of file adapter_search.hpp.

Referenced by InferAdapterSeq().

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

include/algo/sequence/adapter_search.hpp
src/algo/sequence/adapter_search.cpp

Classes

Public Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members