vg::algorithms::GFAzParser Class Reference

#include <gfaz_to_handle.hpp>

Inheritance diagram for vg::algorithms::GFAzParser:

Classes
struct	PendingRGFAVisit

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	prepare_decode ()
void	finish_decode ()
void	on_header (const string &header_line) override
void	on_segment (uint32_t id, const string &sequence, const gfaz::GfaTagList &tags) override
void	on_link (uint32_t from_id, bool from_is_reverse, uint32_t to_id, bool to_is_reverse, const string &overlap, const gfaz::GfaTagList &tags) override
void	on_path (const string &name, const vector< gfaz::NodeId > &visits, const string &overlap, const gfaz::GfaTagList &tags) override
void	on_walk (const string &sample_name, uint32_t haplotype, const string &contig_name, int64_t sequence_start, int64_t sequence_end, const vector< gfaz::NodeId > &visits) override
void	handle_duplicate_paths (char line_type, const function< void(void)> &callback)

Static Private Member Functions
static visit_source_t	make_visit_source (const vector< gfaz::NodeId > &visits)

Private Attributes
vector< PendingRGFAVisit >	pending_rgfa_visits
unordered_map< string, int64_t >	rgfa_path_ranks

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.
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.
using	text_visit_source_t = function<void(const text_visit_iteratee_t&)>
	Callback shape for being a producer of path/walk visits.
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 adapts GFAz's decoded record visitor to vg's shared GFA listener interface.

Member Function Documentation

finish_decode()

void vg::algorithms::GFAzParser::finish_decode ( )

private

handle_duplicate_paths()

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

private

Wrap a function in a handler for GFADuplicatePathError that reports that a line of the given type 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.

make_visit_source()

GFAParser::visit_source_t vg::algorithms::GFAzParser::make_visit_source ( const vector< gfaz::NodeId > & visits )

staticprivate

Translate a vector of GFAz node IDs into a function that produces vg-style rank, id, orientation visit calls.

on_header()

void vg::algorithms::GFAzParser::on_header ( const string & header_line )

overrideprivate

on_link()

void vg::algorithms::GFAzParser::on_link ( uint32_t from_id, bool from_is_reverse, uint32_t to_id, bool to_is_reverse, const string & overlap, const gfaz::GfaTagList & tags )

overrideprivate

on_path()

void vg::algorithms::GFAzParser::on_path ( const string & name, const vector< gfaz::NodeId > & visits, const string & overlap, const gfaz::GfaTagList & tags )

overrideprivate

on_segment()

void vg::algorithms::GFAzParser::on_segment ( uint32_t id, const string & sequence, const gfaz::GfaTagList & tags )

overrideprivate

on_walk()

void vg::algorithms::GFAzParser::on_walk ( const string & sample_name, uint32_t haplotype, const string & contig_name, int64_t sequence_start, int64_t sequence_end, const vector< gfaz::NodeId > & visits )

overrideprivate

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.

prepare_decode()

void vg::algorithms::GFAzParser::prepare_decode ( )

private

Member Data Documentation

pending_rgfa_visits

vector<PendingRGFAVisit> vg::algorithms::GFAzParser::pending_rgfa_visits

private

rgfa_path_ranks

unordered_map<string, int64_t> vg::algorithms::GFAzParser::rgfa_path_ranks

private

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

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