vg::Counts Struct Reference

#include <readfilter.hpp>

Public Types
enum	FilterName {   read = 0 , wrong_name , wrong_refpos , excluded_feature ,   min_score , min_sec_score , max_length , max_overhang ,   min_end_matches , min_mapq , split , repeat ,   defray , defray_all , random , min_base_qual ,   subsequence , proper_pair , unmapped , annotation ,   incorrectly_mapped , first_alignment , max_reads , filtered ,   last }

Public Member Functions
	Counts ()
Counts &	operator+= (const Counts &other)
Counts &	set_paired_any ()
	If any read was filtered, count the other read as filtered.
Counts &	set_paired_all ()
	If not all reads were filtered, count filtered ones as unfiltered.
void	reset ()
void	apply_max_reads (std::atomic< size_t > &counter, const size_t &limit)
void	invert ()
	Invert whether we are kept or not.
bool	keep ()

Public Attributes
vector< size_t >	counts

Member Enumeration Documentation

FilterName

enum vg::Counts::FilterName

Enumerator
read
wrong_name
wrong_refpos
excluded_feature
min_score
min_sec_score
max_length
max_overhang
min_end_matches
min_mapq
split
repeat
defray
defray_all
random
min_base_qual
subsequence
proper_pair
unmapped
annotation
incorrectly_mapped
first_alignment
max_reads
filtered
last

Constructor & Destructor Documentation

Counts()

vg::Counts::Counts ( )

inline

Member Function Documentation

apply_max_reads()

void vg::Counts::apply_max_reads ( std::atomic< size_t > & counter, const size_t & limit )

inline

If currently kept, and the limit is not std:numeric_limits<size_t>::max(), consume space in the counter. If space cannot be consumed in the counter to fit the read (or pair), become un-kept.

invert()

void vg::Counts::invert ( )

inline

Invert whether we are kept or not.

keep()

bool vg::Counts::keep ( )

inline

operator+=()

Counts & vg::Counts::operator+= ( const Counts & other )

inline

reset()

void vg::Counts::reset ( )

inline

set_paired_all()

Counts & vg::Counts::set_paired_all ( )

inline

If not all reads were filtered, count filtered ones as unfiltered.

set_paired_any()

Counts & vg::Counts::set_paired_any ( )

inline

If any read was filtered, count the other read as filtered.

Member Data Documentation

counts

vector<size_t> vg::Counts::counts

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

• src/readfilter.hpp