#include <index_lane_summary.h>

Public Types
typedef std::vector< index_count_summary >	count_summary_vector_t

typedef count_summary_vector_t::reference	reference

typedef count_summary_vector_t::const_reference	const_reference

typedef count_summary_vector_t::iterator	iterator

typedef count_summary_vector_t::const_iterator	const_iterator

typedef count_summary_vector_t::size_type	size_type

typedef ::uint64_t	read_count_t

Public Member Functions
	index_lane_summary (const read_count_t total_reads=0, const read_count_t total_pf_reads=0, const float total_fraction_mapped_reads=0, const float mapped_reads_cv=0, const float min_mapped_reads=0, const float max_mapped_reads=0)

void	resize (const size_type n)

void	reserve (const size_type n)

void	push_back (const index_count_summary &count_summary)

size_type	size () const

iterator	begin ()

iterator	end ()

const_iterator	begin () const

const_iterator	end () const

index_count_summary &	operator[] (const size_type n) INTEROP_THROW_SPEC((model

const index_count_summary &	operator[] (const size_t n) const INTEROP_THROW_SPEC((model

index_count_summary &	at (const size_t n) INTEROP_THROW_SPEC((model

const_reference	at (const size_type n) const INTEROP_THROW_SPEC((model

read_count_t	total_reads () const

read_count_t	total_pf_reads () const

float	total_fraction_mapped_reads () const

float	mapped_reads_cv () const

float	min_mapped_reads () const

float	max_mapped_reads () const

void	sort ()

void	set (const ::uint64_t total_mapped_reads, const read_count_t pf_cluster_count_total, const read_count_t cluster_count_total, const float min_fraction_mapped, const float max_fraction_mapped, const float cv_fraction_mapped)

void	clear ()

Friends
template<class MetricType , int Version>
struct	io::generic_layout

Detailed Description

Summary of metrics for index reads by lane

Member Typedef Documentation

typedef count_summary_vector_t::const_iterator const_iterator

Constant random access iterator to vector of lane summary

typedef count_summary_vector_t::const_reference const_reference

Constant reference to lane summary

typedef std::vector<index_count_summary> count_summary_vector_t

Lane summary vector type

typedef count_summary_vector_t::iterator iterator

Random access iterator to vector of lane summary

typedef ::uint64_t read_count_t

Define a read count type

typedef count_summary_vector_t::reference reference

Reference to lane summary

typedef count_summary_vector_t::size_type size_type

Unsigned integral type (usually size_t)

Constructor & Destructor Documentation

index_lane_summary	(	const read_count_t	total_reads = `0`,
		const read_count_t	total_pf_reads = `0`,
		const float	total_fraction_mapped_reads = `0`,
		const float	mapped_reads_cv = `0`,
		const float	min_mapped_reads = `0`,
		const float	max_mapped_reads = `0`
	)

inline

Constructor

Parameters

total_reads	total clusters
total_pf_reads	total PF clusters
total_fraction_mapped_reads	total fraction of reads mapped
mapped_reads_cv	standard deviation of the mapped reads
min_mapped_reads	minimum of the mapped reads
max_mapped_reads	maximum of the mapped reads

Member Function Documentation

iterator begin ( )

inline

Get random access iterator to start of summaries by read

Returns: random access iterator

const_iterator begin ( ) const

inline

Get constant random access iterator to start of summaries by read

Returns: constant random access iterator

void clear ( )

inline

Clear the lane info

iterator end ( )

inline

Get random access iterator to end of summaries by read

Returns: random access iterator

const_iterator end ( ) const

inline

Get constant random access iterator to end of summaries by read

Returns: constant random access iterator

void push_back ( const index_count_summary & count_summary )

inline

Add a new index count summary

void reserve ( const size_type n )

inline

Reserve space for the number of indexes

Parameters

n	number of indexes

void resize ( const size_type n )

inline

Resize space for the number of indexes

Parameters

n	number of indexes

void set	(	const ::uint64_t	total_mapped_reads,
		const read_count_t	pf_cluster_count_total,
		const read_count_t	cluster_count_total,
		const float	min_fraction_mapped,
		const float	max_fraction_mapped,
		const float	cv_fraction_mapped
	)

inline

Set the data for the lane summary

Parameters

total_mapped_reads	number of reads mapped
pf_cluster_count_total	number of PF clusters
cluster_count_total	number of clusters
min_fraction_mapped	minimum fraction of reads mapped
max_fraction_mapped	maximum fraction of reads mapped
cv_fraction_mapped	coefficient of variation of fraction of reads mapped

size_type size ( ) const

inline

Get number of summaries by read

Returns: number of summaries by read

void sort ( )

inline

Sort the index summaries in each lane

Friends And Related Function Documentation

friend struct io::generic_layout

friend

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

/io/interop/model/summary/index_lane_summary.h

Public Types

Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation