vg
tools for working with variation graphs
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#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::VG * | g_graph |
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
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int8_t* vg::DepthMap::depths |
Map <node_id : offset : depth> or Map <SnarlTraversal : support count>
vg::VG* vg::DepthMap::g_graph |
map<int64_t, uint64_t> vg::DepthMap::node_pos |
uint64_t vg::DepthMap::size |