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

#include <srpe.hpp>

Public Member Functions

 DepthMap (int64_t sz)
 
 DepthMap ()
 
 DepthMap (vg::VG *graph)
 
int8_t get_depth (int64_t node_id, int64_t offset)
 
void set_depth (int64_t node_id, int64_t offset, int8_t d)
 
void increment_depth (int64_t node_id, int64_t offset)
 
void fill_depth (const vg::Path &p)
 

Public Attributes

int8_t * depths
 
uint64_t size
 
map< int64_t, uint64_t > node_pos
 
vg::VGg_graph
 

Detailed Description

Overview: Use the GAM/GAM index and a filter to locate Alignments which may indicate the presence of structural variants at a given site.

Signatures include: Deletions/Insertions: Stacked soft clips (tips) Inversions: mismatched P/E reads( <– && --> rather than the expected ( --> <– ) Duplications: Read depth signals Translocations: Distant read pairs

Constructor & Destructor Documentation

◆ DepthMap() [1/3]

vg::DepthMap::DepthMap ( int64_t  sz)
inline

◆ DepthMap() [2/3]

vg::DepthMap::DepthMap ( )
inline

◆ DepthMap() [3/3]

vg::DepthMap::DepthMap ( vg::VG graph)
inline

Member Function Documentation

◆ fill_depth()

void vg::DepthMap::fill_depth ( const vg::Path p)
inline

◆ get_depth()

int8_t vg::DepthMap::get_depth ( int64_t  node_id,
int64_t  offset 
)
inline

◆ increment_depth()

void vg::DepthMap::increment_depth ( int64_t  node_id,
int64_t  offset 
)
inline

◆ set_depth()

void vg::DepthMap::set_depth ( int64_t  node_id,
int64_t  offset,
int8_t  d 
)
inline

Member Data Documentation

◆ depths

int8_t* vg::DepthMap::depths

Map <node_id : offset : depth> or Map <SnarlTraversal : support count>

◆ g_graph

vg::VG* vg::DepthMap::g_graph

◆ node_pos

map<int64_t, uint64_t> vg::DepthMap::node_pos

◆ size

uint64_t vg::DepthMap::size

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