#include <min_distance.hpp>
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| ChainIndex (id_t parent_id, id_t id_in_parent, id_t end_id, bool rev_in_parent, bool loops, size_t length) |
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| ChainIndex () |
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void | load (istream &in) |
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void | serialize (ostream &out) const |
| Serialize the chain. More...
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int64_t | chain_distance (pair< size_t, bool > start, pair< size_t, bool > end, int64_t startLen, int64_t endLen, bool check_loop=false) const |
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int64_t | chain_length () const |
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void | print_self () const |
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json_t * | chain_to_json () |
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int64_t | loop_distance (pair< size_t, bool > start, pair< size_t, bool > end, int64_t startLen, int64_t endLen) const |
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Stores distances between snarls in a chain
◆ ChainIndex() [1/2]
vg::MinimumDistanceIndex::ChainIndex::ChainIndex |
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id_t |
parent_id, |
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id_t |
id_in_parent, |
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id_t |
end_id, |
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bool |
rev_in_parent, |
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bool |
loops, |
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size_t |
length |
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Constructor for ChainIndex loops is true if the chain loops - the start and end node are the same length is the number of snarls in the chain
◆ ChainIndex() [2/2]
vg::MinimumDistanceIndex::ChainIndex::ChainIndex |
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◆ chain_distance()
int64_t vg::MinimumDistanceIndex::ChainIndex::chain_distance |
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pair< size_t, bool > |
start, |
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pair< size_t, bool > |
end, |
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int64_t |
startLen, |
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int64_t |
endLen, |
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bool |
check_loop = false |
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Distance between two node sides in a chain. size_t values specify the nodes - rank of the node in the chain, bool specifies the direction the node is traversed i.e. if both bools are false, then the distance is between the left side of the start node traversing it forward to the left side of the end node traversing forward. Orientation is relative to the direction the chain is traversed in
◆ chain_length()
int64_t vg::MinimumDistanceIndex::ChainIndex::chain_length |
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const |
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◆ chain_to_json()
json_t * vg::MinimumDistanceIndex::ChainIndex::chain_to_json |
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◆ load()
void vg::MinimumDistanceIndex::ChainIndex::load |
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istream & |
in | ) |
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◆ loop_distance()
int64_t vg::MinimumDistanceIndex::ChainIndex::loop_distance |
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pair< size_t, bool > |
start, |
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pair< size_t, bool > |
end, |
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int64_t |
startLen, |
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int64_t |
endLen |
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Helper function for chainDistance. Used to find the distance in a looping chain by taking the extra loop
◆ print_self()
void vg::MinimumDistanceIndex::ChainIndex::print_self |
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const |
◆ serialize()
void vg::MinimumDistanceIndex::ChainIndex::serialize |
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ostream & |
out | ) |
const |
◆ MinimumDistanceIndex
◆ SnarlSeedClusterer
◆ end_id
id_t vg::MinimumDistanceIndex::ChainIndex::end_id |
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◆ id_in_parent
id_t vg::MinimumDistanceIndex::ChainIndex::id_in_parent |
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◆ is_looping_chain
bool vg::MinimumDistanceIndex::ChainIndex::is_looping_chain |
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◆ loop_fd
int_vector vg::MinimumDistanceIndex::ChainIndex::loop_fd |
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For each boundary node of snarls in the chain, the distance from the start of the node traversing forward to the end of the same node traversing backwards -directions relative to the direction the node is traversed in the chain
◆ loop_rev
int_vector vg::MinimumDistanceIndex::ChainIndex::loop_rev |
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For each boundary node of snarls in the chain, the distance from the end of the node traversing backward to the start of the same node traversing forward
◆ max_width
int64_t vg::MinimumDistanceIndex::ChainIndex::max_width |
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◆ parent_id
id_t vg::MinimumDistanceIndex::ChainIndex::parent_id |
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id of parent snarl of the chain 0 if top level chain
◆ prefix_sum
int_vector vg::MinimumDistanceIndex::ChainIndex::prefix_sum |
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Dist from start of chain to start of each boundary node of all snarls in the chain The first value should be 0 according to this scheme but it is the length of the first node in the chain. Similarly, an extra value is stored at the end of the vector that is the length of the entire chain
◆ rev_in_parent
bool vg::MinimumDistanceIndex::ChainIndex::rev_in_parent |
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The documentation for this class was generated from the following files: