#include <gfaz_to_handle.hpp>

Inheritance diagram for vg::algorithms::GFAzParser:

Public Member Functions
void	parse (istream &in) override

void	parse (const string &filename) override

Public Member Functions inherited from vg::algorithms::GFAParser
GFAIDMapInfo &	id_map ()

const GFAIDMapInfo &	id_map () const

virtual	~GFAParser ()=default

Static Public Member Functions
static bool	looks_like_gfaz (const string &filename)

static bool	has_magic (const char *buffer, size_t length)

Static Public Member Functions inherited from vg::algorithms::GFAParser
static string	extract (const chars_t &range)

static size_t	length (const chars_t &range)

static bool	empty (const chars_t &range)

static chars_t	as_chars (const string &value)

Private Member Functions
void	handle_duplicate_paths (char line_type, const std::function< void(void)> &callback)

Additional Inherited Members
Public Types inherited from vg::algorithms::GFAParser
using	cursor_t = string::const_iterator

using	chars_t = pair< cursor_t, cursor_t >

using	tag_list_t = vector< string >

using	visit_iteratee_t = function< bool(int64_t rank, nid_t node_id, bool is_reverse)>

using	visit_source_t = function< void(const visit_iteratee_t &)>

Public Attributes inherited from vg::algorithms::GFAParser
vector< std::function< void(const tag_list_t &tags)> >	header_listeners
	These listeners are called for the header line(s), if any. More...

vector< std::function< void(nid_t id, const chars_t &sequence, const tag_list_t &tags)> >	node_listeners

vector< std::function< void(nid_t from, bool from_is_reverse, nid_t to, bool to_is_reverse, const chars_t &overlap, const tag_list_t &tags)> >	edge_listeners

vector< std::function< void(const string &name, const visit_source_t &visits, const tag_list_t &tags)> >	path_listeners

vector< std::function< void(const string &sample_name, int64_t haplotype, const string &contig_name, const pair< int64_t, int64_t > &subrange, const visit_source_t &visits, const tag_list_t &tags)> >	walk_listeners

vector< std::function< void(nid_t id, int64_t offset, size_t length, const string &path_name, int64_t path_rank)> >	rgfa_listeners

unique_ptr< GFAIDMapInfo >	internal_id_map

GFAIDMapInfo *	external_id_map = nullptr

int64_t	max_rgfa_rank = -1

bool	stop_on_duplicate_paths = false

Protected Types inherited from vg::algorithms::GFAParser
using	text_visit_iteratee_t = function< bool(int64_t rank, const chars_t &node_name, bool is_reverse)>
	Callback shape for receiving path/walk visits internally. More...

using	text_visit_source_t = function< void(const text_visit_iteratee_t &)>
	Callback shape for being a producer of path/walk visits. More...

Protected Member Functions inherited from vg::algorithms::GFAParser
text_visit_iteratee_t	wrap (const visit_iteratee_t &iteratee) const

visit_source_t	wrap (const text_visit_source_t &source) const

Static Protected Member Functions inherited from vg::algorithms::GFAParser
static tag_list_t	parse_tags (const chars_t &tag_range)

static tuple< tag_list_t >	parse_h (const string &h_line)

static tuple< string, chars_t, tag_list_t >	parse_s (const string &s_line)

static tuple< string, bool, string, bool, chars_t, tag_list_t >	parse_l (const string &l_line)

static tuple< string, chars_t, chars_t, tag_list_t >	parse_p (const string &p_line)

static tuple< string, size_t, string, pair< int64_t, int64_t >, chars_t, tag_list_t >	parse_w (const string &p_line)

static void	scan_p_visits (const chars_t &visit_range, function< bool(int64_t rank, const chars_t &node_name, bool is_reverse)> visit_step)

static void	scan_w_visits (const chars_t &visit_range, function< bool(int64_t rank, const chars_t &node_name, bool is_reverse)> visit_step)

static void	scan_visits (const chars_t &visit_range, char line_type, function< bool(int64_t rank, const chars_t &node_name, bool is_reverse)> visit_step)

static bool	decode_rgfa_tags (const tag_list_t &tags, string out_name=nullptr, int64_t out_offset=nullptr, int64_t *out_rank=nullptr)

static nid_t	assign_new_sequence_id (const string &str, GFAIDMapInfo &id_map_info)

static nid_t	find_existing_sequence_id (std::string_view str, const GFAIDMapInfo &id_map_info)

Detailed Description

GFAZ parser implementation that emits the same listener events from decompressed GFAZ data.

Member Function Documentation

◆ handle_duplicate_paths()

void vg::algorithms::GFAzParser::handle_duplicate_paths	(	char	line_type,
		const std::function< void(void)> &	callback
	)

private

Wrap a function in a handler for GFADuplicatePathError that reports that a line of the given line tyoe is being skipped.

◆ has_magic()

bool vg::algorithms::GFAzParser::has_magic	(	const char *	buffer,
		size_t	length
	)

static

Return true if the first sizeof(uint32_t) bytes of the buffer encode the GFAz magic number.

◆ looks_like_gfaz()

bool vg::algorithms::GFAzParser::looks_like_gfaz ( const string & filename )

static

Return true if the named file begins with the GFAz magic number. Returns false for stdin ("-") or empty filenames.

◆ parse() [1/2]

void vg::algorithms::GFAzParser::parse ( const string & filename )

overridevirtual

Parse GFA from the given filename. The default implementation opens the file as a text GFA stream and calls the stream parser.

Reimplemented from vg::algorithms::GFAParser.

◆ parse() [2/2]

void vg::algorithms::GFAzParser::parse ( istream & in )

overridevirtual

Parse GFA from the given stream.

Implements vg::algorithms::GFAParser.

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

src/algorithms/gfaz_to_handle.hpp
src/algorithms/gfaz_to_handle.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions