#include <surjector.hpp>

Inheritance diagram for vg::Surjector:

Public Types
using	path_chunk_t = pair< pair< string::const_iterator, string::const_iterator >, path_t >
	a local type that represents a read interval matched to a portion of the alignment path More...

Public Member Functions
	Surjector (const PathPositionHandleGraph *graph)

Alignment	surject (const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const

vector< Alignment >	multi_surject (const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const
	Same as above, but include alignments to all paths instead of only the optimal one. More...

Alignment	surject (const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const

vector< Alignment >	multi_surject (const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const
	Same as above, but include alignments to all paths instead of only the optimal one. More...

multipath_alignment_t	surject (const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const

vector< multipath_alignment_t >	multi_surject (const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const
	Same as above, but include alignments to all paths instead of only the optimal one. More...

template<>
int32_t	get_score (const Alignment &aln)

template<>
int32_t	get_score (const multipath_alignment_t &mp_aln)

Public Member Functions inherited from vg::AlignerClient
virtual void	set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)
	Set all the aligner scoring parameters and create the stored aligner instances. More...

virtual void	set_alignment_scores (std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)

virtual void	set_alignment_scores (const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)

Public Attributes
int64_t	min_splice_length = 20
	the minimum length deletion that the spliced algorithm will interpret as a splice event More...

int64_t	dominated_path_chunk_diff = 10

int64_t	min_splice_repair_length = 250
	the minimum length apparent intron that we will try to repair More...

size_t	max_subgraph_bases = 100 * 1024
	How big of a graph in bp should we ever try to align against for realigning surjection? More...

int64_t	min_fold_coverage_for_downsample = 8
	in spliced surject, downsample if the base-wise average coverage by chunks is this high More...

int64_t	downsample_coverage = 16
	while downsampling, try to get down to this coverage on each base More...

int64_t	min_shift_for_prune = 32 * 1024

int64_t	shift_prune_diff = 16 * 1024

atomic_flag	warned_about_subgraph_size = ATOMIC_FLAG_INIT
	And have we complained about hitting it? More...

bool	prune_suspicious_anchors = false

int64_t	max_tail_anchor_prune = 4

double	low_complexity_p_value = .001

size_t	max_anchors = 200

bool	annotate_with_all_path_scores = false

Public Attributes inherited from vg::AlignerClient
bool	adjust_alignments_for_base_quality = false

Protected Member Functions
void	surject_internal (const Alignment source_aln, const multipath_alignment_t source_mp_aln, vector< Alignment > alns_out, vector< multipath_alignment_t > mp_alns_out, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool all_paths, bool allow_negative_scores, bool preserve_deletions) const

Alignment	realigning_surject (const PathPositionHandleGraph graph, const Alignment &source, const path_handle_t &path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool sinks_are_anchors=false, bool sources_are_anchors=false, vector< pair< step_handle_t, step_handle_t >> all_path_ranges_out=nullptr) const

multipath_alignment_t	spliced_surject (const PathPositionHandleGraph *path_position_graph, const string &src_sequence, const string &src_quality, const int32_t src_mapping_quality, const path_handle_t &path_handle, bool rev_strand, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool deletions_as_splices) const

unordered_map< pair< path_handle_t, bool >, pair< vector< path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > >	extract_overlapping_paths (const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const
	get the chunks of the alignment path that follow the given reference paths More...

unordered_map< pair< path_handle_t, bool >, pair< vector< path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > >	extract_overlapping_paths (const PathPositionHandleGraph *graph, const multipath_alignment_t &source, const unordered_set< path_handle_t > &surjection_paths, unordered_map< pair< path_handle_t, bool >, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const
	same semantics except for a multipath alignment More...

void	filter_redundant_path_chunks (bool path_rev, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const

pair< size_t, size_t >	compute_path_interval (const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, bool no_left_expansion, bool no_right_expansion) const

void	set_path_position (const PathPositionHandleGraph *graph, const pos_t &init_surj_pos, const pos_t &final_surj_pos, const step_handle_t &range_begin, const step_handle_t &range_end, bool rev_strand, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const
	use the graph position bounds and the path range bounds to assign a path position to a surjected read More...

template<class AlnType >
string	path_score_annotations (const unordered_map< pair< path_handle_t, bool >, pair< AlnType, pair< step_handle_t, step_handle_t >>> &surjections) const

vector< vector< size_t > >	reverse_adjacencies (const vector< vector< size_t >> &adj) const
	reverses an adjacency list More...

vector< size_t >	connected_components (const vector< vector< size_t >> &adj, const vector< vector< size_t >> &rev_adj, size_t *num_comps_out) const

vector< vector< size_t > >	transitive_reduction (const vector< vector< size_t >> &adj) const
	returns the transitive reduction of a topologically sorted DAG's adjacency list More...

vector< vector< size_t > >	remove_dominated_chunks (const string &src_sequence, const vector< vector< size_t >> &adj, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const
	eliminate any path chunks that have the exact same colinearities as another but are much shorter More...

void	cut_anchors (bool rev_strand, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const
	if any anchors overlap each other, cut the second at the implied overlap position More...

void	downsample_chunks (const string &src_sequence, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const
	if there are too many chunks, downsample to a given level More...

vector< pair< vector< size_t >, vector< size_t > > >	find_constriction_bicliques (const vector< vector< size_t >> &adj, const string &src_sequence, const string &src_quality, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, const vector< tuple< size_t, size_t, int32_t >> &connections) const

void	prune_unconnectable (vector< vector< size_t >> &adj, vector< vector< tuple< size_t, int32_t, bool >>> &splice_adj, vector< size_t > &component, vector< vector< size_t >> &comp_groups, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks) const

Protected Member Functions inherited from vg::AlignerClient
	AlignerClient (double gc_content_estimate=vg::default_gc_content)

const GSSWAligner *	get_aligner (bool have_qualities=true) const

const QualAdjAligner *	get_qual_adj_aligner () const

const Aligner *	get_regular_aligner () const

Static Protected Member Functions
static Alignment	make_null_alignment (const Alignment &source)
	make a sentinel meant to indicate an unmapped read More...

static multipath_alignment_t	make_null_mp_alignment (const string &src_sequence, const string &src_quality)

template<class AlnType >
static int32_t	get_score (const AlnType &aln)

Protected Attributes
const PathPositionHandleGraph *	graph = nullptr
	the graph we're surjecting onto More...

Additional Inherited Members
Static Public Member Functions inherited from vg::AlignerClient
static int8_t *	parse_matrix (std::istream &matrix_stream)
	Allocates an array to hold a 4x4 substitution matrix and returns it. More...

Member Typedef Documentation

◆ path_chunk_t

using vg::Surjector::path_chunk_t = pair<pair<string::const_iterator, string::const_iterator>, path_t>

a local type that represents a read interval matched to a portion of the alignment path

Constructor & Destructor Documentation

◆ Surjector()

vg::Surjector::Surjector ( const PathPositionHandleGraph * graph )

Member Function Documentation

◆ compute_path_interval()

pair< size_t, size_t > vg::Surjector::compute_path_interval	(	const PathPositionHandleGraph *	graph,
		const Alignment &	source,
		path_handle_t	path_handle,
		bool	rev_strand,
		const vector< path_chunk_t > &	path_chunks,
		const vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		bool	no_left_expansion,
		bool	no_right_expansion
	)		const

protected

Compute the widest end-inclusive interval of path positions that the realigned sequence could align to, or an interval where start > end if there are no path chunks.

◆ connected_components()

vector< size_t > vg::Surjector::connected_components	(	const vector< vector< size_t >> &	adj,
		const vector< vector< size_t >> &	rev_adj,
		size_t *	num_comps_out
	)		const

protected

returns a vector assignming each node to a connectd component, requires both the forward and reverse adjacency lists. optionally also returns the total number of components

◆ cut_anchors()

void vg::Surjector::cut_anchors	(	bool	rev_strand,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		vector< tuple< size_t, size_t, int32_t >> &	connections
	)		const

protected

if any anchors overlap each other, cut the second at the implied overlap position

◆ downsample_chunks()

void vg::Surjector::downsample_chunks	(	const string &	src_sequence,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		vector< tuple< size_t, size_t, int32_t >> &	connections
	)		const

protected

if there are too many chunks, downsample to a given level

◆ extract_overlapping_paths() [1/2]

unordered_map< pair< path_handle_t, bool >, pair< vector< Surjector::path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > > vg::Surjector::extract_overlapping_paths	(	const PathPositionHandleGraph *	graph,
		const Alignment &	source,
		const unordered_set< path_handle_t > &	surjection_paths
	)		const

protected

get the chunks of the alignment path that follow the given reference paths

◆ extract_overlapping_paths() [2/2]

unordered_map< pair< path_handle_t, bool >, pair< vector< Surjector::path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > > vg::Surjector::extract_overlapping_paths	(	const PathPositionHandleGraph *	graph,
		const multipath_alignment_t &	source,
		const unordered_set< path_handle_t > &	surjection_paths,
		unordered_map< pair< path_handle_t, bool >, vector< tuple< size_t, size_t, int32_t >>> &	connections_out
	)		const

protected

same semantics except for a multipath alignment

◆ filter_redundant_path_chunks()

void vg::Surjector::filter_redundant_path_chunks	(	bool	path_rev,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		vector< tuple< size_t, size_t, int32_t >> &	connections
	)		const

protected

remove any path chunks and corresponding ref chunks that are identical to a longer path chunk over the region where they overlap

◆ find_constriction_bicliques()

vector< pair< vector< size_t >, vector< size_t > > > vg::Surjector::find_constriction_bicliques	(	const vector< vector< size_t >> &	adj,
		const string &	src_sequence,
		const string &	src_quality,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		const vector< tuple< size_t, size_t, int32_t >> &	connections
	)		const

protected

returns all sets of chunks such that 1) all of chunks on the left set abut all of the chunks on the right set on the read, 2) all source-to-sink paths in the connected component go through an edge between the left and right sides, 3) all of the chunks that do not have a connection between them are fully connected (i.e. form a biclique)

◆ get_score() [1/3]

template<>

int32_t vg::Surjector::get_score ( const Alignment & aln )

◆ get_score() [2/3]

template<class AlnType >

static int32_t vg::Surjector::get_score ( const AlnType & aln )

staticprotected

◆ get_score() [3/3]

template<>

int32_t vg::Surjector::get_score ( const multipath_alignment_t & mp_aln )

◆ make_null_alignment()

Alignment vg::Surjector::make_null_alignment ( const Alignment & source )

staticprotected

make a sentinel meant to indicate an unmapped read

◆ make_null_mp_alignment()

multipath_alignment_t vg::Surjector::make_null_mp_alignment	(	const string &	src_sequence,
		const string &	src_quality
	)

staticprotected

◆ multi_surject() [1/3]

vector< Alignment > vg::Surjector::multi_surject	(	const Alignment &	source,
		const unordered_set< path_handle_t > &	paths,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Same as above, but include alignments to all paths instead of only the optimal one.

◆ multi_surject() [2/3]

vector< Alignment > vg::Surjector::multi_surject	(	const Alignment &	source,
		const unordered_set< path_handle_t > &	paths,
		vector< tuple< string, int64_t, bool >> &	positions_out,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Same as above, but include alignments to all paths instead of only the optimal one.

◆ multi_surject() [3/3]

vector< multipath_alignment_t > vg::Surjector::multi_surject	(	const multipath_alignment_t &	source,
		const unordered_set< path_handle_t > &	paths,
		vector< tuple< string, int64_t, bool >> &	positions_out,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Same as above, but include alignments to all paths instead of only the optimal one.

◆ path_score_annotations()

template<class AlnType >

string vg::Surjector::path_score_annotations ( const unordered_map< pair< path_handle_t, bool >, pair< AlnType, pair< step_handle_t, step_handle_t >>> & surjections ) const

protected

◆ prune_unconnectable()

void vg::Surjector::prune_unconnectable	(	vector< vector< size_t >> &	adj,
		vector< vector< tuple< size_t, int32_t, bool >>> &	splice_adj,
		vector< size_t > &	component,
		vector< vector< size_t >> &	comp_groups,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks
	)		const

protected

◆ realigning_surject()

Alignment vg::Surjector::realigning_surject	(	const PathPositionHandleGraph *	graph,
		const Alignment &	source,
		const path_handle_t &	path_handle,
		bool	rev_strand,
		const vector< path_chunk_t > &	path_chunks,
		const vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		pair< step_handle_t, step_handle_t > &	path_range_out,
		bool	allow_negative_scores,
		bool	preserve_N_alignments = `false`,
		bool	sinks_are_anchors = `false`,
		bool	sources_are_anchors = `false`,
		vector< pair< step_handle_t, step_handle_t >> *	all_path_ranges_out = `nullptr`
	)		const

protected

◆ remove_dominated_chunks()

vector< vector< size_t > > vg::Surjector::remove_dominated_chunks	(	const string &	src_sequence,
		const vector< vector< size_t >> &	adj,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		vector< tuple< size_t, size_t, int32_t >> &	connections
	)		const

protected

eliminate any path chunks that have the exact same colinearities as another but are much shorter

◆ reverse_adjacencies()

vector< vector< size_t > > vg::Surjector::reverse_adjacencies ( const vector< vector< size_t >> & adj ) const

protected

reverses an adjacency list

◆ set_path_position()

void vg::Surjector::set_path_position	(	const PathPositionHandleGraph *	graph,
		const pos_t &	init_surj_pos,
		const pos_t &	final_surj_pos,
		const step_handle_t &	range_begin,
		const step_handle_t &	range_end,
		bool	rev_strand,
		string &	path_name_out,
		int64_t &	path_pos_out,
		bool &	path_rev_out
	)		const

protected

use the graph position bounds and the path range bounds to assign a path position to a surjected read

◆ spliced_surject()

multipath_alignment_t vg::Surjector::spliced_surject	(	const PathPositionHandleGraph *	path_position_graph,
		const string &	src_sequence,
		const string &	src_quality,
		const int32_t	src_mapping_quality,
		const path_handle_t &	path_handle,
		bool	rev_strand,
		vector< path_chunk_t > &	path_chunks,
		vector< pair< step_handle_t, step_handle_t >> &	ref_chunks,
		vector< tuple< size_t, size_t, int32_t >> &	connections,
		pair< step_handle_t, step_handle_t > &	path_range_out,
		bool	allow_negative_scores,
		bool	deletions_as_splices
	)		const

protected

◆ surject() [1/3]

Alignment vg::Surjector::surject	(	const Alignment &	source,
		const unordered_set< path_handle_t > &	paths,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Extract the portions of an alignment that are on a chosen set of paths and try to align realign the portions that are off of the chosen paths to the intervening path segments to obtain an alignment that is fully restricted to the paths.

Replaces the alignment's refpos with the path name, position, and strand the alignment has been surjected to.

Optionally either allow softclips so that the alignment has a nonnegative score on the path or require the full-length alignment, possibly creating a negative score.

Also optionally leaves deletions against the reference path in the final alignment (useful for splicing).

◆ surject() [2/3]

Alignment vg::Surjector::surject	(	const Alignment &	source,
		const unordered_set< path_handle_t > &	paths,
		string &	path_name_out,
		int64_t &	path_pos_out,
		bool &	path_rev_out,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Extract the portions of an alignment that are on a chosen set of paths and try to align realign the portions that are off of the chosen paths to the intervening path segments to obtain an alignment that is fully restricted to the paths.

Also returns the path name, position, and strand of the new alignment.

Optionally either allow softclips so that the alignment has a nonnegative score on the path or require the full-length alignment, possibly creating a negative score.

Also optionally leaves deletions against the reference path in the final alignment (useful for splicing).

◆ surject() [3/3]

multipath_alignment_t vg::Surjector::surject	(	const multipath_alignment_t &	source,
		const unordered_set< path_handle_t > &	paths,
		string &	path_name_out,
		int64_t &	path_pos_out,
		bool &	path_rev_out,
		bool	allow_negative_scores = `false`,
		bool	preserve_deletions = `false`
	)		const

Same semantics as with alignments except that connections are always preserved as splices. The output consists of a multipath alignment with a single path, separated by splices (either from large deletions or from connections)

◆ surject_internal()

void vg::Surjector::surject_internal	(	const Alignment *	source_aln,
		const multipath_alignment_t *	source_mp_aln,
		vector< Alignment > *	alns_out,
		vector< multipath_alignment_t > *	mp_alns_out,
		const unordered_set< path_handle_t > &	paths,
		vector< tuple< string, int64_t, bool >> &	positions_out,
		bool	all_paths,
		bool	allow_negative_scores,
		bool	preserve_deletions
	)		const

protected

◆ transitive_reduction()

vector< vector< size_t > > vg::Surjector::transitive_reduction ( const vector< vector< size_t >> & adj ) const

protected

returns the transitive reduction of a topologically sorted DAG's adjacency list

Member Data Documentation

◆ annotate_with_all_path_scores

bool vg::Surjector::annotate_with_all_path_scores = false

◆ dominated_path_chunk_diff

int64_t vg::Surjector::dominated_path_chunk_diff = 10

◆ downsample_coverage

int64_t vg::Surjector::downsample_coverage = 16

while downsampling, try to get down to this coverage on each base

◆ graph

const PathPositionHandleGraph* vg::Surjector::graph = nullptr

protected

the graph we're surjecting onto

◆ low_complexity_p_value

double vg::Surjector::low_complexity_p_value = .001

◆ max_anchors

size_t vg::Surjector::max_anchors = 200

How many anchors (per path) will we use when surjecting using anchors? Excessive anchors will be pruned away.

◆ max_subgraph_bases

size_t vg::Surjector::max_subgraph_bases = 100 * 1024

How big of a graph in bp should we ever try to align against for realigning surjection?

◆ max_tail_anchor_prune

int64_t vg::Surjector::max_tail_anchor_prune = 4

◆ min_fold_coverage_for_downsample

int64_t vg::Surjector::min_fold_coverage_for_downsample = 8

in spliced surject, downsample if the base-wise average coverage by chunks is this high

◆ min_shift_for_prune

int64_t vg::Surjector::min_shift_for_prune = 32 * 1024

◆ min_splice_length

int64_t vg::Surjector::min_splice_length = 20

the minimum length deletion that the spliced algorithm will interpret as a splice event

◆ min_splice_repair_length

int64_t vg::Surjector::min_splice_repair_length = 250

the minimum length apparent intron that we will try to repair

◆ prune_suspicious_anchors

bool vg::Surjector::prune_suspicious_anchors = false

◆ shift_prune_diff

int64_t vg::Surjector::shift_prune_diff = 16 * 1024

◆ warned_about_subgraph_size

atomic_flag vg::Surjector::warned_about_subgraph_size = ATOMIC_FLAG_INIT

mutable

And have we complained about hitting it?

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

src/surjector.hpp
src/surjector.cpp

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Typedef Documentation

◆ path_chunk_t

Constructor & Destructor Documentation

◆ Surjector()

Member Function Documentation

◆ compute_path_interval()

◆ connected_components()

◆ cut_anchors()

◆ downsample_chunks()

◆ extract_overlapping_paths() [1/2]

◆ extract_overlapping_paths() [2/2]

◆ filter_redundant_path_chunks()

◆ find_constriction_bicliques()

◆ get_score() [1/3]

◆ get_score() [2/3]

◆ get_score() [3/3]

◆ make_null_alignment()

◆ make_null_mp_alignment()

◆ multi_surject() [1/3]

◆ multi_surject() [2/3]

◆ multi_surject() [3/3]

◆ path_score_annotations()

◆ prune_unconnectable()

◆ realigning_surject()

◆ remove_dominated_chunks()

◆ reverse_adjacencies()

◆ set_path_position()

◆ spliced_surject()

◆ surject() [1/3]

◆ surject() [2/3]

◆ surject() [3/3]

◆ surject_internal()

◆ transitive_reduction()

Member Data Documentation

◆ annotate_with_all_path_scores

◆ dominated_path_chunk_diff

◆ downsample_coverage

◆ graph

◆ low_complexity_p_value

◆ max_anchors

◆ max_subgraph_bases

◆ max_tail_anchor_prune

◆ min_fold_coverage_for_downsample

◆ min_shift_for_prune

◆ min_splice_length

◆ min_splice_repair_length

◆ prune_suspicious_anchors

◆ shift_prune_diff

◆ warned_about_subgraph_size