minimizer_main.cpp File Reference

#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include <algorithm>
#include <iostream>
#include <vector>
#include <getopt.h>
#include <omp.h>
#include "../gbwtgraph_helper.hpp"
#include "../gbwt_helper.hpp"
#include "../index_registry.hpp"
#include "../utility.hpp"
#include "../handle.hpp"
#include "../snarl_distance_index.hpp"
#include <gbwtgraph/index.h>

Functions
int	get_default_threads ()
size_t	estimate_hash_table_size (const gbwtgraph::GBZ &gbz, bool progress)
void	help_minimizer (char **argv)
int	main_minimizer (int argc, char **argv)
size_t	trailing_zeros (size_t value)

Variables
constexpr int	DEFAULT_MAX_THREADS = 16
constexpr size_t	DEFAULT_THRESHOLD = 500
constexpr size_t	DEFAULT_ITERATIONS = 3
constexpr size_t	MAX_ITERATIONS = gbwtgraph::MinimizerHeader::FLAG_WEIGHT_MASK >> gbwtgraph::MinimizerHeader::FLAG_WEIGHT_OFFSET
constexpr size_t	HASH_TABLE_MIN_WIDTH = 10
constexpr size_t	HASH_TABLE_MAX_WIDTH = 36

Detailed Description

Defines the "vg minimizer" subcommand, which builds the minimizer index.

The index contains the lexicographically smallest kmer in a window of w successive kmers and their reverse complements. If the kmer contains characters other than A, C, G, and T, it will not be indexed.

The index contains either all or haplotype-consistent minimizers. Indexing all minimizers from complex graph regions can take a long time (e.g. tens of hours vs 5-10 minutes for 1000GP), because many windows have the same minimizer. As the total number of minimizers is manageable (e.g. 1.5x more for 1000GP) it should be possible to develop a better algorithm for finding the minimizers.

A quick idea for indexing the entire graph:

• For each node v, extract the subgraph for the windows starting in v.
• Extract all k'-mers from the subgraph and use them to determine where the minimizers can start.

Function Documentation

estimate_hash_table_size()

size_t estimate_hash_table_size	(	const gbwtgraph::GBZ &	gbz,
		bool	progress
	)

get_default_threads()

int get_default_threads

(

)

help_minimizer()

void help_minimizer

(

char **

argv

)

main_minimizer()

int main_minimizer	(	int	argc,
		char **	argv
	)

trailing_zeros()

size_t trailing_zeros

(

size_t

value

)

Variable Documentation

DEFAULT_ITERATIONS

constexpr size_t DEFAULT_ITERATIONS = 3

constexpr

DEFAULT_MAX_THREADS

constexpr int DEFAULT_MAX_THREADS = 16

constexpr

DEFAULT_THRESHOLD

constexpr size_t DEFAULT_THRESHOLD = 500

constexpr

HASH_TABLE_MAX_WIDTH

constexpr size_t HASH_TABLE_MAX_WIDTH = 36

constexpr

HASH_TABLE_MIN_WIDTH

constexpr size_t HASH_TABLE_MIN_WIDTH = 10

constexpr

MAX_ITERATIONS

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

constexpr