#include <rare_variant_simplifier.hpp>
Inheritance diagram for vg::RareVariantSimplifier:
Public Member Functions | |
| RareVariantSimplifier (MutablePathDeletableHandleGraph &graph, VcfBuffer &variant_source) | |
| void | simplify () |
| Simplify the graph. More... | |
 Public Member Functions inherited from vg::Progressive | |
| void | preload_progress (const string &message) |
| void | create_progress (const string &message, long count) |
| void | create_progress (long count) |
| void | ensure_progress (long count) |
| void | update_progress (long i) |
| void | increment_progress () |
| void | destroy_progress (void) |
Public Attributes | |
| double | min_frequency_to_keep = 0 |
| Keep variants at this total alt allele frequency or higher. More... | |
| size_t | min_count_to_keep = 0 |
| Public Attributes inherited from vg::Progressive | |
| bool | show_progress = false |
Protected Attributes | |
| MutablePathDeletableHandleGraph & | graph |
| Holds a reference to the graph we're simplifying. More... | |
| VcfBuffer & | variant_source |
| Holds a reference to the variant buffer we are getting avriants from. More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from vg::Progressive | |
| static void | with_progress (bool show_progress, const std::string &task, const std::function< void(const std::function< void(size_t, size_t)> &progress)> &callback) |
Detailed Description
A class that can be used to simplify a graph, by removing rare variants' alt and ref paths and their exclusively-used nodes.
Constructor & Destructor Documentation
◆ RareVariantSimplifier()
| vg::RareVariantSimplifier::RareVariantSimplifier | ( | MutablePathDeletableHandleGraph & | graph, |
| VcfBuffer & | variant_source | ||
| ) |
Make a simplifier that simplifies the given graph in place, using variants read using the given buffer.
Member Function Documentation
◆ simplify()
| void vg::RareVariantSimplifier::simplify | ( | ) |
Simplify the graph.
Member Data Documentation
◆ graph
|
protected |
Holds a reference to the graph we're simplifying.
◆ min_count_to_keep
| size_t vg::RareVariantSimplifier::min_count_to_keep = 0 |
Keep variants with this total alt allele count or higher. AND'd with the frequency condition.
◆ min_frequency_to_keep
| double vg::RareVariantSimplifier::min_frequency_to_keep = 0 |
Keep variants at this total alt allele frequency or higher.
◆ variant_source
|
protected |
Holds a reference to the variant buffer we are getting avriants from.
The documentation for this class was generated from the following files:
