vg
tools for working with variation graphs
Public Member Functions | Public Attributes | List of all members
vg::SRPE Class Reference

#include <srpe.hpp>

Public Member Functions

void call_svs_paired_end (vg::VG *graph, ifstream &gamstream, vector< BREAKPOINT > &bps, string refpath="")
 
void call_svs_split_read (vg::VG *graph, ifstream &gamstream, vector< BREAKPOINT > &bps, string refpath="")
 
void call_svs (string graphfile, string gamfile, string refpath)
 
double discordance_score (vector< Alignment > alns, VG *subgraph)
 
void aln_to_bseq (Alignment &a, fml_seq1_t *read)
 
void assemble (vector< Alignment > alns, vector< fml_utg_t > &unitigs)
 
void assemble (string refpath, int64_t start_pos, int64_t end_pos, vector< fml_utg_t > &unitigs)
 
void assemble (int64_t node_id, int64_t offset, int window_size)
 

Public Attributes

vector< string > ref_names
 
map< string, PathIndexpindexes
 
vector< pair< int, int > > intervals
 
bool overlapping_refs = false
 
DepthMap depth
 
vg::Filter ff
 
map< string, Alignmentname_to_aln
 
map< string, string > aln_to_mate
 
vg::VGgraph
 
int max_reads = 125
 

Member Function Documentation

◆ aln_to_bseq()

void vg::SRPE::aln_to_bseq ( Alignment a,
fml_seq1_t *  read 
)

◆ assemble() [1/3]

void vg::SRPE::assemble ( int64_t  node_id,
int64_t  offset,
int  window_size 
)

◆ assemble() [2/3]

void vg::SRPE::assemble ( string  refpath,
int64_t  start_pos,
int64_t  end_pos,
vector< fml_utg_t > &  unitigs 
)

◆ assemble() [3/3]

void vg::SRPE::assemble ( vector< Alignment alns,
vector< fml_utg_t > &  unitigs 
)

function assemble inputs: a vector of Alignments to be assembled (based on their sequences) outputs:

◆ call_svs()

void vg::SRPE::call_svs ( string  graphfile,
string  gamfile,
string  refpath 
)

◆ call_svs_paired_end()

void vg::SRPE::call_svs_paired_end ( vg::VG graph,
ifstream &  gamstream,
vector< BREAKPOINT > &  bps,
string  refpath = "" 
)

◆ call_svs_split_read()

void vg::SRPE::call_svs_split_read ( vg::VG graph,
ifstream &  gamstream,
vector< BREAKPOINT > &  bps,
string  refpath = "" 
)

◆ discordance_score()

double vg::SRPE::discordance_score ( vector< Alignment alns,
VG subgraph 
)

Member Data Documentation

◆ aln_to_mate

map<string, string> vg::SRPE::aln_to_mate

◆ depth

DepthMap vg::SRPE::depth

◆ ff

vg::Filter vg::SRPE::ff

◆ graph

vg::VG* vg::SRPE::graph

◆ intervals

vector<pair<int, int> > vg::SRPE::intervals

◆ max_reads

int vg::SRPE::max_reads = 125

◆ name_to_aln

map<string, Alignment> vg::SRPE::name_to_aln

◆ overlapping_refs

bool vg::SRPE::overlapping_refs = false

◆ pindexes

map<string, PathIndex> vg::SRPE::pindexes

◆ ref_names

vector<string> vg::SRPE::ref_names

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