vg::MinimizerIndexParameters Struct Reference

Minimizer index construction parameters. More...

#include <gbwtgraph_helper.hpp>

Public Types
enum	PayloadType { PAYLOAD_NONE, PAYLOAD_ZIPCODES, PAYLOAD_ZIPCODES_WITH_PATHS }

Public Member Functions
MinimizerIndexParameters &	minimizers (size_t k, size_t w)
	Sets minimizer parameters. More...
MinimizerIndexParameters &	syncmers (size_t k, size_t s)
	Sets syncmer parameters. More...
MinimizerIndexParameters &	with_paths (bool paths_in_payload=true)
	Includes path information in the payload. More...
MinimizerIndexParameters &	weighted (bool use_weighted_minimizers, size_t threshold=DEFAULT_THRESHOLD, size_t iterations=DEFAULT_ITERATIONS)
	Sets weighted minimizer parameters. More...
MinimizerIndexParameters &	kmer_counting (bool space_efficient_counting=false, size_t hash_table_width=0)
	Sets k-mer counting parameters. More...
MinimizerIndexParameters &	verbose (bool progress=true)
	Sets progress printing. More...
std::string	validate () const
	Returns an error message if the parameters are invalid. More...

Static Public Member Functions
static std::string	payload_str (PayloadType type)

Public Attributes
size_t	k = gbwtgraph::DefaultMinimizerIndex::key_type::KMER_LENGTH
	k-mer length. More...
size_t	w_or_s = gbwtgraph::DefaultMinimizerIndex::key_type::WINDOW_LENGTH
	Window length (with minimizers) or s-mer length (with syncmers). More...
bool	use_syncmers = false
	Whether to use syncmers instead of minimizers. More...
bool	paths_in_payload = false
bool	use_weighted_minimizers = false
	Whether to use weighted minimizers (cannot be used with syncmers). More...
size_t	threshold = DEFAULT_THRESHOLD
	Downweight kmers with more than this many hits. More...
size_t	iterations = DEFAULT_ITERATIONS
	Number of iterations for weighted minimizer calculation. More...
bool	space_efficient_counting = false
	Whether to use the space-efficient k-mer counting algorithm with weighted minimizers. More...
size_t	hash_table_width = 0
	Initial hash table width (in bits) for kmer counting (0 = guess). More...
bool	progress = false
	Print progress information during construction. More...

Static Public Attributes
constexpr static size_t	DEFAULT_THRESHOLD = 500
	Default for threshold. Should be the same as Giraffe hard hit cap. More...
constexpr static size_t	DEFAULT_ITERATIONS = 3
	Default for iterations. More...
constexpr static size_t	MAX_ITERATIONS = gbwtgraph::MinimizerHeader::FLAG_WEIGHT_MASK >> gbwtgraph::MinimizerHeader::FLAG_WEIGHT_OFFSET
	Maximum allowed value for iterations. More...
constexpr static size_t	HASH_TABLE_MIN_WIDTH = 10
	Lower bound for hash_table_width. More...
constexpr static size_t	HASH_TABLE_MAX_WIDTH = 36
	Upper bound for hash_table_width. More...
constexpr static size_t	ZIPCODE_PAYLOAD_SIZE = sizeof(ZipCode::payload_type) / sizeof(gbwtgraph::KmerEncoding::code_type)
	Number of words used for a zipcode payload. More...
const static std::string	PAYLOAD_KEY = "payload"
	Tag used to indicate the payload type in the minimizer index. More...

Detailed Description

Minimizer index construction parameters.

Member Enumeration Documentation

PayloadType

enum vg::MinimizerIndexParameters::PayloadType

Enumerator
PAYLOAD_NONE	No payload.
PAYLOAD_ZIPCODES	Zipcode payload.
PAYLOAD_ZIPCODES_WITH_PATHS	Zipcode payload with path information.

Member Function Documentation

kmer_counting()

MinimizerIndexParameters& vg::MinimizerIndexParameters::kmer_counting ( bool  space_efficient_counting = false, size_t  hash_table_width = 0  )

inline

Sets k-mer counting parameters.

minimizers()

MinimizerIndexParameters& vg::MinimizerIndexParameters::minimizers ( size_t  k, size_t  w  )

inline

Sets minimizer parameters.

payload_str()

std::string vg::MinimizerIndexParameters::payload_str ( PayloadType  type )

static

Returns a string representation of the payload type. This will be used as a tag value in the minimizer index.

syncmers()

MinimizerIndexParameters& vg::MinimizerIndexParameters::syncmers ( size_t  k, size_t  s  )

inline

Sets syncmer parameters.

validate()

std::string vg::MinimizerIndexParameters::validate

(

)

const

Returns an error message if the parameters are invalid.

verbose()

MinimizerIndexParameters& vg::MinimizerIndexParameters::verbose ( bool  progress = true )

inline

Sets progress printing.

weighted()

MinimizerIndexParameters& vg::MinimizerIndexParameters::weighted ( bool  use_weighted_minimizers, size_t  threshold = DEFAULT_THRESHOLD, size_t  iterations = DEFAULT_ITERATIONS  )

inline

Sets weighted minimizer parameters.

with_paths()

MinimizerIndexParameters& vg::MinimizerIndexParameters::with_paths ( bool  paths_in_payload = true )

inline

Includes path information in the payload.

Member Data Documentation

DEFAULT_ITERATIONS

constexpr size_t vg::MinimizerIndexParameters::DEFAULT_ITERATIONS = 3

staticconstexpr

Default for iterations.

DEFAULT_THRESHOLD

constexpr size_t vg::MinimizerIndexParameters::DEFAULT_THRESHOLD = 500

staticconstexpr

Default for threshold. Should be the same as Giraffe hard hit cap.

HASH_TABLE_MAX_WIDTH

constexpr size_t vg::MinimizerIndexParameters::HASH_TABLE_MAX_WIDTH = 36

staticconstexpr

Upper bound for hash_table_width.

HASH_TABLE_MIN_WIDTH

constexpr size_t vg::MinimizerIndexParameters::HASH_TABLE_MIN_WIDTH = 10

staticconstexpr

Lower bound for hash_table_width.

hash_table_width

size_t vg::MinimizerIndexParameters::hash_table_width = 0

Initial hash table width (in bits) for kmer counting (0 = guess).

iterations

size_t vg::MinimizerIndexParameters::iterations = DEFAULT_ITERATIONS

Number of iterations for weighted minimizer calculation.

k

size_t vg::MinimizerIndexParameters::k = gbwtgraph::DefaultMinimizerIndex::key_type::KMER_LENGTH

k-mer length.

MAX_ITERATIONS

constexpr size_t vg::MinimizerIndexParameters::MAX_ITERATIONS = gbwtgraph::MinimizerHeader::FLAG_WEIGHT_MASK >> gbwtgraph::MinimizerHeader::FLAG_WEIGHT_OFFSET

staticconstexpr

Maximum allowed value for iterations.

paths_in_payload

bool vg::MinimizerIndexParameters::paths_in_payload = false

Whether to include path information in the payload (for recombination-aware mapping). Ignored if there is no zipcode payload.

PAYLOAD_KEY

const std::string vg::MinimizerIndexParameters::PAYLOAD_KEY = "payload"

static

Tag used to indicate the payload type in the minimizer index.

progress

bool vg::MinimizerIndexParameters::progress = false

Print progress information during construction.

space_efficient_counting

bool vg::MinimizerIndexParameters::space_efficient_counting = false

Whether to use the space-efficient k-mer counting algorithm with weighted minimizers.

threshold

size_t vg::MinimizerIndexParameters::threshold = DEFAULT_THRESHOLD

Downweight kmers with more than this many hits.

use_syncmers

bool vg::MinimizerIndexParameters::use_syncmers = false

Whether to use syncmers instead of minimizers.

use_weighted_minimizers

bool vg::MinimizerIndexParameters::use_weighted_minimizers = false

Whether to use weighted minimizers (cannot be used with syncmers).

w_or_s

size_t vg::MinimizerIndexParameters::w_or_s = gbwtgraph::DefaultMinimizerIndex::key_type::WINDOW_LENGTH

Window length (with minimizers) or s-mer length (with syncmers).

ZIPCODE_PAYLOAD_SIZE

constexpr size_t vg::MinimizerIndexParameters::ZIPCODE_PAYLOAD_SIZE = sizeof(ZipCode::payload_type) / sizeof(gbwtgraph::KmerEncoding::code_type)

staticconstexpr

Number of words used for a zipcode payload.

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

• src/gbwtgraph_helper.hpp
• src/gbwtgraph_helper.cpp