vg
tools for working with variation graphs
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#include <snarl_caller.hpp>
Public Member Functions | |
PoissonSupportSnarlCaller (const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder, const algorithms::BinnedDepthIndex &depth_index) | |
virtual | ~PoissonSupportSnarlCaller () |
virtual vector< int > | 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 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... | |
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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... | |
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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... | |
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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 | |
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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... | |
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
vg::PoissonSupportSnarlCaller::PoissonSupportSnarlCaller | ( | const PathHandleGraph & | graph, |
SnarlManager & | snarl_manager, | ||
TraversalSupportFinder & | support_finder, | ||
const algorithms::BinnedDepthIndex & | depth_index | ||
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Get the genotype of a site.
Implements vg::SnarlCaller.
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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
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Rank supports.
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Define any header fields needed by the above.
Implements vg::SnarlCaller.
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Update INFO and FORMAT fields of the called variant.
Reimplemented from vg::SupportBasedSnarlCaller.
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Baseline mapping error rate (gets added to the standard error from coverage)
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Map path name to <mean, std_err> of depth coverage from the packer.
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padding to apply wrt to longest traversal to snarl ranges when looking up binned depth
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Consider up to the top-k traversals (based on support) for genotyping.
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Consider up to the tom-m secondary traversals (based on support) for each top traversal (so at most top_k * top_m considered)