#include <snarl_caller.hpp>
Inheritance diagram for vg::PoissonSupportSnarlCaller:
Classes | |
| struct | PoissonCallInfo |
Public Member Functions | |
| PoissonSupportSnarlCaller (const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder, const algorithms::BinnedDepthIndex &depth_index) | |
| virtual | ~PoissonSupportSnarlCaller () |
| virtual pair< vector< int >, unique_ptr< CallInfo > > | genotype (const Snarl &snarl, const vector< SnarlTraversal > &traversals, int ref_trav_idx, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_range) |
| Get the genotype of a site. More... | |
| virtual void | update_vcf_info (const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const unique_ptr< CallInfo > &call_info, const string &sample_name, vcflib::Variant &variant) |
| Update INFO and FORMAT fields of the called variant. More... | |
| virtual void | update_vcf_header (string &header) const |
| Define any header fields needed by the above. More... | |
 Public Member Functions inherited from vg::SupportBasedSnarlCaller | |
| SupportBasedSnarlCaller (const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder) | |
| virtual | ~SupportBasedSnarlCaller () |
| void | set_min_supports (double min_mad_for_call, double min_support_for_call, double min_site_support) |
| Set some of the parameters. More... | |
| const TraversalSupportFinder & | get_support_finder () const |
| Get the traversal support finder. More... | |
| virtual int | get_min_total_support_for_call () const |
| Get the minimum total support for call. More... | |
| virtual function< bool(const SnarlTraversal &, int iteration)> | get_skip_allele_fn () const |
| Use min_alt_path_support threshold as cutoff. More... | |
| Public Member Functions inherited from vg::SnarlCaller | |
| virtual | ~SnarlCaller () |
Protected Member Functions | |
| double | genotype_likelihood (const vector< int > &genotype, const vector< SnarlTraversal > &traversals, const set< int > &trav_subset, int ref_trav_idx, double exp_depth, double depth_err) |
| vector< int > | rank_by_support (const vector< Support > &supports) |
| Rank supports. More... | |
Protected Attributes | |
| double | baseline_mapping_error = 0.005 |
| Baseline mapping error rate (gets added to the standard error from coverage) More... | |
| size_t | top_k = 20 |
| Consider up to the top-k traversals (based on support) for genotyping. More... | |
| size_t | top_m = 100 |
| double | depth_padding_factor = 1. |
| padding to apply wrt to longest traversal to snarl ranges when looking up binned depth More... | |
| const algorithms::BinnedDepthIndex & | depth_index |
| Map path name to <mean, std_err> of depth coverage from the packer. More... | |
| Protected Attributes inherited from vg::SupportBasedSnarlCaller | |
| const PathHandleGraph & | graph |
| SnarlManager & | snarl_manager |
| TraversalSupportFinder & | support_finder |
| Get support from traversals. More... | |
| int | min_total_support_for_call = 1 |
| size_t | min_mad_for_filter = 1 |
| size_t | min_site_depth = 3 |
| double | min_alt_path_support = 0.5 |
Additional Inherited Members | |
| Static Protected Member Functions inherited from vg::SupportBasedSnarlCaller | |
| static int | get_best_support (const vector< Support > &supports, const vector< int > &skips) |
| Get the best support out of a list of supports, ignoring skips. More... | |
| static double | support_val (const Support &support) |
| Relic from old code. More... | |
Detailed Description
Find the genotype of some traversals in a site using read support and a Poisson model based on expected depth. Inspired, in part, by Paragraph, which uses a similar approach for genotyping break points
Constructor & Destructor Documentation
◆ PoissonSupportSnarlCaller()
| vg::PoissonSupportSnarlCaller::PoissonSupportSnarlCaller | ( | const PathHandleGraph & | graph, |
| SnarlManager & | snarl_manager, | ||
| TraversalSupportFinder & | support_finder, | ||
| const algorithms::BinnedDepthIndex & | depth_index | ||
| ) |
◆ ~PoissonSupportSnarlCaller()
|
virtual |
Member Function Documentation
◆ genotype()
|
virtual |
Get the genotype of a site.
Implements vg::SnarlCaller.
◆ genotype_likelihood()
|
protected |
Compute likelihood of genotype as product of poisson probabilities P[allele1] * P[allle2] * P[uncalled alleles] Homozygous alleles are split into two, with half support each The (natural) logoarithm is returned If trav_subset is not empty, traversals outside that set (and genotype) will be ignored to save time
◆ rank_by_support()
|
protected |
Rank supports.
◆ update_vcf_header()
|
virtual |
Define any header fields needed by the above.
Implements vg::SnarlCaller.
◆ update_vcf_info()
|
virtual |
Update INFO and FORMAT fields of the called variant.
Reimplemented from vg::SupportBasedSnarlCaller.
Member Data Documentation
◆ baseline_mapping_error
|
protected |
Baseline mapping error rate (gets added to the standard error from coverage)
◆ depth_index
|
protected |
Map path name to <mean, std_err> of depth coverage from the packer.
◆ depth_padding_factor
|
protected |
padding to apply wrt to longest traversal to snarl ranges when looking up binned depth
◆ top_k
|
protected |
Consider up to the top-k traversals (based on support) for genotyping.
◆ top_m
|
protected |
Consider up to the tom-m secondary traversals (based on support) for each top traversal (so at most top_k * top_m considered)
The documentation for this class was generated from the following files:
- src/snarl_caller.hpp
- src/snarl_caller.cpp
