#include <seed_clusterer.hpp>
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tuple< vector< structures::UnionFind >, structures::UnionFind > | cluster_seeds_internal (const vector< const vector< Seed > * > &all_seeds, int64_t read_distance_limit, int64_t fragment_distance_limit=0) const |
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void | get_nodes (TreeState &tree_state, vector< hash_map< size_t, vector< pair< NetgraphNode, NodeClusters >>>> &snarl_to_nodes_by_level) const |
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void | cluster_snarl_level (TreeState &tree_state, size_t depth) const |
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void | cluster_chain_level (TreeState &tree_state, size_t depth) const |
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NodeClusters | cluster_one_node (TreeState &tree_state, id_t node_id, int64_t node_length) const |
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NodeClusters | cluster_one_snarl (TreeState &tree_state, size_t snarl_index_i) const |
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NodeClusters | cluster_one_chain (TreeState &tree_state, size_t chain_i, size_t depth) const |
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void | cluster_only_top_level_chain_seeds (TreeState &tree_state, vector< pair< size_t, size_t >> &seed_clusters) const |
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hash_set< pair< size_t, size_t > > | cluster_simple_snarl (TreeState &tree_state, vector< tuple< id_t, bool, int64_t, int64_t, int64_t >> nodes, int64_t loop_left, int64_t loop_right, int64_t snarl_length) const |
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◆ ChildNodeType
Enumerator |
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CHAIN | |
SNARL | |
NODE | |
◆ SnarlSeedClusterer()
◆ cluster_chain_level()
void vg::SnarlSeedClusterer::cluster_chain_level |
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TreeState & |
tree_state, |
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size_t |
depth |
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) |
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private |
◆ cluster_one_chain()
◆ cluster_one_node()
◆ cluster_one_snarl()
◆ cluster_only_top_level_chain_seeds()
void vg::SnarlSeedClusterer::cluster_only_top_level_chain_seeds |
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TreeState & |
tree_state, |
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vector< pair< size_t, size_t >> & |
seed_clusters |
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) |
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private |
◆ cluster_seeds() [1/2]
Given a vector of seeds and a distance limit,.
◆ cluster_seeds() [2/2]
vector< vector< SnarlSeedClusterer::Cluster > > vg::SnarlSeedClusterer::cluster_seeds |
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const vector< vector< Seed >> & |
all_seeds, |
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int64_t |
read_distance_limit, |
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int64_t |
fragment_distance_limit = 0 |
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) |
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The same thing, but for paired end reads.
◆ cluster_seeds_internal()
tuple< vector< structures::UnionFind >, structures::UnionFind > vg::SnarlSeedClusterer::cluster_seeds_internal |
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const vector< const vector< Seed > * > & |
all_seeds, |
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int64_t |
read_distance_limit, |
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int64_t |
fragment_distance_limit = 0 |
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) |
| const |
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private |
◆ cluster_simple_snarl()
hash_set< pair< size_t, size_t > > vg::SnarlSeedClusterer::cluster_simple_snarl |
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TreeState & |
tree_state, |
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vector< tuple< id_t, bool, int64_t, int64_t, int64_t >> |
nodes, |
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int64_t |
loop_left, |
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int64_t |
loop_right, |
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int64_t |
snarl_length |
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) |
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◆ cluster_snarl_level()
void vg::SnarlSeedClusterer::cluster_snarl_level |
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TreeState & |
tree_state, |
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size_t |
depth |
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private |
◆ get_nodes()
◆ typeToString()
static string vg::SnarlSeedClusterer::typeToString |
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ChildNodeType |
t | ) |
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inlinestaticprivate |
◆ dist_index
The documentation for this class was generated from the following files: