#include <homogenizer.hpp>
◆ cut_nonref_tips()
void Homogenizer::cut_nonref_tips |
( |
vg::VG * |
graph | ) |
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private |
Remove non-reference tips from the graph.
◆ cut_tips() [1/2]
void Homogenizer::cut_tips |
( |
vector< id_t > |
tip_ids, |
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vg::VG * |
graph |
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) |
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private |
Remove specific nodes and their edges from the graph
◆ cut_tips() [2/2]
void Homogenizer::cut_tips |
( |
vg::VG * |
graph | ) |
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private |
Remove all tips from the graph. WARNING: may cut head/tail nodes.
◆ find_non_ref_tips()
◆ find_tips()
Find tips (nodes with an indegree/outdegree of 0 in the graph
◆ homogenize() [1/2]
Locates tips in the graph and tries to generate a single edge / node to represent them. This edge is then added, the offending sequences are remapped, and the process is repeated until the graph becomes stable.
Reindex graph and reset mapper
◆ homogenize() [2/2]
Pattern for SV homogenization
- Locate SV-indicating reads with Sift. Save them in a gam file
- index that gam with index -d dbname -N
- Send those reads here - for each possible position Find reads supporting that position Generate candidate edges and nodes Remap reads locally (w/in some subgraph containing the SV) Score it somehow Check the reads again for SV signatures.
◆ remap()
remap a set of Alignments to the graph
◆ translator
The documentation for this class was generated from the following files: