#include <deconstructor.hpp>
◆ Deconstructor()
vg::Deconstructor::Deconstructor |
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◆ ~Deconstructor()
vg::Deconstructor::~Deconstructor |
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◆ check_max_nodes()
bool vg::Deconstructor::check_max_nodes |
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const Snarl * |
snarl | ) |
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◆ choose_traversals()
pair< vector< int >, bool > vg::Deconstructor::choose_traversals |
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const vector< int > & |
travs, |
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const vector< int > & |
trav_to_allele, |
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const vector< string > & |
trav_to_name |
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◆ deconstruct()
void vg::Deconstructor::deconstruct |
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vector< string > |
ref_paths, |
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const PathPositionHandleGraph * |
graph, |
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SnarlManager * |
snarl_manager, |
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bool |
path_restricted_traversals, |
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int |
ploidy, |
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const unordered_map< string, string > * |
path_to_sample = nullptr |
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Convenience wrapper function for deconstruction of multiple paths.
◆ deconstruct_site()
bool vg::Deconstructor::deconstruct_site |
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const Snarl * |
site | ) |
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◆ explicit_exhaustive_traversals()
vector< SnarlTraversal > vg::Deconstructor::explicit_exhaustive_traversals |
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const Snarl * |
snarl | ) |
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◆ get_alleles()
vector< int > vg::Deconstructor::get_alleles |
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vcflib::Variant & |
v, |
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const vector< SnarlTraversal > & |
travs, |
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int |
ref_path_idx, |
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char |
prev_char, |
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bool |
use_start |
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Takes in a vector of snarltraversals returns their sequences as a vector<string> returns a boolean hasRef if a reference path is present, hasRef is set to true and the first string in the vector is the reference allele otherwise, hasRef is set to false and all strings are alt alleles.
◆ get_genotypes()
void vg::Deconstructor::get_genotypes |
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vcflib::Variant & |
v, |
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const vector< string > & |
names, |
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const vector< int > & |
trav_to_allele |
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◆ graph
◆ max_nodes_for_exhaustive
int vg::Deconstructor::max_nodes_for_exhaustive = 100 |
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◆ outvcf
vcflib::VariantCallFile vg::Deconstructor::outvcf |
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◆ path_restricted
bool vg::Deconstructor::path_restricted = false |
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◆ path_to_sample
const unordered_map<string, string>* vg::Deconstructor::path_to_sample |
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◆ path_trav_finder
◆ ploidy
int vg::Deconstructor::ploidy |
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◆ ref_paths
set<string> vg::Deconstructor::ref_paths |
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◆ sample_names
set<string> vg::Deconstructor::sample_names |
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◆ snarl_manager
◆ trav_finder
The documentation for this class was generated from the following files: