mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
771 lines
18 KiB
C
771 lines
18 KiB
C
#ifndef __POA_PARSER__
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#define __POA_PARSER__
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#include <stdint.h>
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#include "Hash_Table.h"
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#include "Process_Read.h"
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typedef struct
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{
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long long beg;
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///end is the index of next input data, instead of the index of last data
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long long end;
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long long length;
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long long size;
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long long* buffer;
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} Queue;
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inline void init_Queue(Queue* q)
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{
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q->beg = 0;
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q->end = 0;
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q->length = 0;
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q->size = 20;
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q->buffer = (long long*)malloc(sizeof(long long)*q->size);
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}
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inline void clear_Queue(Queue* q)
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{
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q->beg = 0;
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q->end = 0;
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q->length = 0;
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}
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inline void destory_Queue(Queue* q)
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{
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free(q->buffer);
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}
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inline int is_empty_Queue(Queue* q)
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{
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///end is the index of next input data, instead of the index of last data
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if(q->beg == q->end)
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{
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return 1;
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}
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else
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{
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return 0;
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}
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}
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inline int is_full_Queue(Queue* q)
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{
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///end is the index of next input data, instead of the index of last data
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if(q->end < q->size)
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{
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return 0;
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}
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else
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{
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return 1;
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}
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}
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inline void push_to_Queue(Queue* q, long long nodeID)
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{
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if(is_full_Queue(q))
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{
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long long move_length = q->beg;
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///end is the index of next input data, instead of the index of last data
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long long current_length = q->end - q->beg;
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///recalloc directly
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if(move_length == 0)
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{
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q->size = q->size * 2;
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q->buffer = (long long*)realloc(q->buffer, q->size*sizeof(long long));
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}
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else
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{
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///won't overlap
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if(current_length <= move_length)
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{
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memcpy(q->buffer, q->buffer+q->beg, sizeof(long long)*current_length);
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}
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else///may overlap
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{
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memmove(q->buffer, q->buffer+q->beg, sizeof(long long)*current_length);
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}
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q->beg = 0;
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q->end = current_length;
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}
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}
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q->buffer[q->end] = nodeID;
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q->end++;
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}
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inline int pop_from_Queue(Queue* q, long long* nodeID)
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{
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if(is_empty_Queue(q))
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{
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(*nodeID) = -1;
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return 0;
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}
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else
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{
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(*nodeID) = q->buffer[q->beg];
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q->beg++;
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return 1;
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}
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}
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typedef struct
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{
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uint64_t in_node;
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uint64_t out_node;
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///0 is match，1 is mismatch，2 means y has more bases, 3 means x has more bases
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uint64_t weight;
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uint64_t num_insertions;
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uint64_t length;
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uint64_t self_edge_ID;
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uint64_t reverse_edge_ID;
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} Edge;
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typedef struct
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{
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Edge* list;
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uint64_t size;
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uint64_t length;
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uint64_t delete_length;
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} Edge_alloc;
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#define Real_Length(X) ((X).length - (X).delete_length)
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#define Input_Edges(Node) ((Node).insertion_edges)
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#define Output_Edges(Node) ((Node).deletion_edges)
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#define G_Node(G, Node) ((G).g_nodes.list[(Node)])
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#define If_Node_Exist(Node) ((Node).base != 'D')
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#define If_Edge_Exist(E) ((E).out_node != (uint64_t)-1)
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#define Visit(E) (E).length
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typedef struct
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{
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long long index;
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} RSet;
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inline void clear_RSet(RSet* set)
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{
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set->index = 0;
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}
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typedef struct
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{
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uint64_t ID;
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uint64_t weight;
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///number of deletion end with current node
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uint64_t num_insertions;
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char base;
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Edge_alloc mismatch_edges;
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Edge_alloc deletion_edges;
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Edge_alloc insertion_edges;
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} Node;
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typedef struct
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{
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uint64_t* list;
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uint8_t* visit;
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uint64_t size;
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uint64_t length;
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uint64_t* iterative_buffer;
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uint8_t* iterative_buffer_visit;
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uint64_t iterative_i;
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} topo_Sorting_buffer;
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typedef struct
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{
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///has a indivial start node 0
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Node* list;
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topo_Sorting_buffer sort;
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uint64_t size;
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uint64_t length;
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uint64_t delete_length;
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} Node_alloc;
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typedef struct
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{
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uint64_t g_n_nodes;
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uint64_t g_n_edges;
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uint64_t g_next_nodeID;
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Node_alloc g_nodes;
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Queue node_q;
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char* seq;
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uint64_t seqID;
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uint64_t s_start_nodeID;
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uint64_t s_end_nodeID;
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} Graph;
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int add_and_check_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag);
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void add_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag);
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int remove_and_check_bi_direction_edge_from_nodes(Graph* graph, Node* in_node, Node* out_node);
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int remove_and_check_bi_direction_edge_from_edge(Graph* graph, Edge* e);
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inline int Pop_Node(Graph* DAGCon, Node** node)
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{
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long long nodeID = 0;
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int return_flag = pop_from_Queue(&(DAGCon->node_q), &nodeID);
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(*node) = &(G_Node(*DAGCon, nodeID));
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return return_flag;
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}
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inline int Push_Node(Graph* DAGCon, Node** node)
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{
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push_to_Queue(&(DAGCon->node_q), (**node).ID);
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return 1;
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}
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inline int getInputNodes(RSet* set, Graph* graph, Node* node, Node** get_Node)
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{
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if(set->index >= (long long)Input_Edges(*node).length)
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{
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return 0;
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}
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///skip all deleted edges
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while (
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set->index < (long long)Input_Edges(*node).length
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&&
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!(If_Edge_Exist(Input_Edges(*node).list[set->index]))
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)
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{
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set->index++;
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}
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if(
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set->index < (long long)Input_Edges(*node).length
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&&
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If_Edge_Exist(Input_Edges(*node).list[set->index])
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)
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{
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(*get_Node) = &(G_Node((*graph), Input_Edges(*node).list[set->index].in_node));
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set->index++;
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return 1;
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}
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else
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{
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return 0;
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}
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}
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inline int getInputEdges(RSet* set, Graph* graph, Node* node, Edge** get_Edge)
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{
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if(set->index >= (long long)Input_Edges(*node).length)
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{
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return 0;
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}
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///skip all deleted edges
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while (
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set->index < (long long)Input_Edges(*node).length
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&&
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!(If_Edge_Exist(Input_Edges(*node).list[set->index]))
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)
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{
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set->index++;
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}
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if(
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set->index < (long long)Input_Edges(*node).length
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&&
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If_Edge_Exist(Input_Edges(*node).list[set->index])
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)
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{
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(*get_Edge) = &(Input_Edges(*node).list[set->index]);
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set->index++;
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return 1;
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}
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else
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{
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return 0;
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}
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}
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inline int getOutputNodes(RSet* set, Graph* graph, Node* node, Node** get_Node)
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{
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if(set->index >= (long long)Output_Edges(*node).length)
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{
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return 0;
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}
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///skip all deleted edges
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while (
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set->index < (long long)Output_Edges(*node).length
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&&
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!(If_Edge_Exist(Output_Edges(*node).list[set->index]))
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)
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{
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set->index++;
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}
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if(set->index < (long long)Output_Edges(*node).length &&
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If_Edge_Exist(Output_Edges(*node).list[set->index]))
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{
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(*get_Node) = &(G_Node((*graph), Output_Edges(*node).list[set->index].out_node));
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set->index++;
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return 1;
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}
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else
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{
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return 0;
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}
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}
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inline int getOutputEdges(RSet* set, Graph* graph, Node* node, Edge** get_Edge)
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{
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if(set->index >= (long long)Output_Edges(*node).length)
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{
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return 0;
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}
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///skip all deleted edges
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while (
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set->index < (long long)Output_Edges(*node).length
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&&
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!(If_Edge_Exist(Output_Edges(*node).list[set->index]))
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)
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{
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set->index++;
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}
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if(set->index < (long long)Output_Edges(*node).length &&
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If_Edge_Exist(Output_Edges(*node).list[set->index]))
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{
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(*get_Edge) = &(Output_Edges(*node).list[set->index]);
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set->index++;
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return 1;
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}
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else
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{
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return 0;
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}
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}
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inline void get_bi_direction_edges(Graph* DAGCon, Edge* edge, Edge** e_forward, Edge** e_backward)
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{
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long long in_node = edge->in_node;
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long long out_node = edge->out_node;
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if(
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edge->self_edge_ID < Output_Edges(G_Node(*DAGCon, in_node)).length
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&&
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(long long)Output_Edges(G_Node(*DAGCon, in_node)).list[edge->self_edge_ID].in_node == in_node
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&&
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(long long)Output_Edges(G_Node(*DAGCon, in_node)).list[edge->self_edge_ID].out_node == out_node
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)
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{
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(*e_forward) = &(Output_Edges(G_Node(*DAGCon, in_node)).list[edge->self_edge_ID]);
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(*e_backward) = &(Input_Edges(G_Node(*DAGCon, out_node)).list[edge->reverse_edge_ID]);
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}
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else
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{
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(*e_forward) = &(Output_Edges(G_Node(*DAGCon, in_node)).list[edge->reverse_edge_ID]);
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(*e_backward) = &(Input_Edges(G_Node(*DAGCon, out_node)).list[edge->self_edge_ID]);
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}
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}
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inline long long get_bi_Edge(Graph* DAGCon, Node* inNode, Node* outNode, Edge** e_forward, Edge** e_backward)
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{
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Edge* e;
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RSet iter;
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clear_RSet(&iter);
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if(If_Node_Exist(*inNode) && If_Node_Exist(*outNode))
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{
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//find in-edge of outNode
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while(getInputEdges(&iter, DAGCon, outNode, &e))
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{
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if(e->in_node == inNode->ID)
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{
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get_bi_direction_edges(DAGCon, e, e_forward, e_backward);
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return 1;
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}
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}
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}
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return 0;
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}
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inline long long get_Edge_Weight(Graph* DAGCon, Node* inNode, Node* outNode)
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{
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Edge* e_forward = NULL;
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Edge* e_backward = NULL;
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get_bi_Edge(DAGCon, inNode, outNode, &e_forward, &e_backward);
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return e_forward->weight;
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}
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void init_Edge_alloc(Edge_alloc* list);
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void clear_Edge_alloc(Edge_alloc* list);
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void destory_Edge_alloc(Edge_alloc* list);
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void append_Edge_alloc(Edge_alloc* list, uint64_t in_node, uint64_t out_node, uint64_t weight, uint64_t length);
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void init_Node_alloc(Node_alloc* list);
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void destory_Node_alloc(Node_alloc* list);
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void clear_Node_alloc(Node_alloc* list);
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uint64_t append_Node_alloc(Node_alloc* list, char base);
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uint64_t* get_Topo_Sort_Order(Node_alloc* list, int need_sort);
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void init_Graph(Graph* g);
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void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long* startID, long long* endID);
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void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
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char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end);
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void destory_Graph(Graph* g);
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void clear_Graph(Graph* g);
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void Perform_POA(Graph* g, overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read);
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uint64_t inline add_Node_Graph(Graph* g, char base)
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{
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return append_Node_alloc(&g->g_nodes, base);
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}
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inline Node* add_Node_DAGCon(Graph* g, char base)
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{
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return &(G_Node(*g, append_Node_alloc(&g->g_nodes, base)));
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}
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///to delete a node
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///1. set the corresponding base to be 'D'
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///2. remove all related edges
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///2. clear all related edges
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///3. g_nodes.delete_length++, please do not substract g_nodes.length
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uint64_t inline delete_Node_DAGCon(Graph* g, Node* node)
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{
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g->g_nodes.delete_length++;
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g->g_nodes.list[(*node).ID].base = 'D';
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g->g_nodes.list[(*node).ID].num_insertions = (uint64_t)-1;
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g->g_nodes.list[(*node).ID].weight = (uint64_t)-1;
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RSet iter;
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Edge* e;
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clear_RSet(&iter);
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while (getOutputEdges(&iter, g, node, &e))
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{
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remove_and_check_bi_direction_edge_from_edge(g, e);
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}
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clear_RSet(&iter);
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while (getInputEdges(&iter, g, node, &e))
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{
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remove_and_check_bi_direction_edge_from_edge(g, e);
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}
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clear_Edge_alloc(&(g->g_nodes.list[(*node).ID].insertion_edges));
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clear_Edge_alloc(&(g->g_nodes.list[(*node).ID].mismatch_edges));
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clear_Edge_alloc(&(g->g_nodes.list[(*node).ID].deletion_edges));
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return 1;
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}
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///just for mimatch edges
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inline void add_mismatchEdge_weight(Graph* g, uint64_t in_node, char base, int last_operation)
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{
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long long i = 0;
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long long nodeID;
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Edge_alloc* edge = &(g->g_nodes.list[in_node].mismatch_edges);
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for (i = 0; i < (long long)edge->length; i++)
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{
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nodeID = edge->list[i].out_node;
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if(g->g_nodes.list[nodeID].base == base)
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{
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edge->list[i].weight++;
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///if last operation is insertion
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if (last_operation == 2)
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{
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edge->list[i].num_insertions++;
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}
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break;
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}
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}
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///there are no such edge
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if (i == (long long)edge->length)
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{
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nodeID = add_Node_Graph(g, base);
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///the length of match edge is 0, while the length of mismatch edge is 1
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append_Edge_alloc(edge, in_node, nodeID, 1, 1);
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///if last operation is insertion
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if (last_operation == 2)
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{
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edge->list[edge->length - 1].num_insertions++;
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}
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///add the mismatch_edges of new node to the backbone
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append_Edge_alloc(&(g->g_nodes.list[nodeID].mismatch_edges), nodeID, in_node + 1, 1, 0);
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}
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}
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inline void add_single_deletionEdge_weight(Graph* g, long long alignNodeID, long long nextNodeID, uint64_t edge_length)
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{
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long long i = 0;
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long long nodeID;
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Edge_alloc* edge = &(g->g_nodes.list[alignNodeID].deletion_edges);
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for (i = 0; i < (long long)edge->length; i++)
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{
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nodeID = edge->list[i].out_node;
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if(nodeID == nextNodeID)
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{
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edge->list[i].weight++;
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break;
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}
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}
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///there are no such edge
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if (i == (long long)edge->length)
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{
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append_Edge_alloc(edge, alignNodeID, nextNodeID, 1, edge_length);
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}
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}
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|
||
inline void add_deletionEdge_weight(Graph* g, long long alignNodeID, long long deletion_length)
|
||
{
|
||
long long i;
|
||
for (i = 0; i < deletion_length; i++)
|
||
{
|
||
add_single_deletionEdge_weight(g, alignNodeID + i, alignNodeID + i + 1, 0);
|
||
}
|
||
|
||
}
|
||
|
||
|
||
inline int getEdge(Graph* g, Edge_alloc* edge, uint64_t edge_length, char base)
|
||
{
|
||
long long i = 0;
|
||
long long nodeID;
|
||
|
||
for (i = 0; i < (long long)edge->length; i++)
|
||
{
|
||
if (edge->list[i].length == edge_length)
|
||
{
|
||
nodeID = edge->list[i].out_node;
|
||
if(g->g_nodes.list[nodeID].base == base)
|
||
{
|
||
return i;
|
||
}
|
||
}
|
||
}
|
||
|
||
return -1;
|
||
}
|
||
|
||
|
||
inline int get_insertion_Edges(Graph* g, Edge_alloc* edge, uint64_t edge_length, char* bases)
|
||
{
|
||
long long i = 0;
|
||
long long nodeID;
|
||
long long edgeID;
|
||
|
||
if (edge_length < 1)
|
||
{
|
||
return -1;
|
||
}
|
||
|
||
|
||
edgeID = getEdge(g, edge, edge_length, bases[0]);
|
||
|
||
long long return_edgeID = edgeID;
|
||
|
||
if(edgeID == -1)
|
||
{
|
||
return -1;
|
||
}
|
||
|
||
|
||
Edge_alloc* new_edge = edge;
|
||
|
||
for (i = 1; i < (long long)edge_length; i++)
|
||
{
|
||
nodeID = new_edge->list[edgeID].out_node;
|
||
new_edge = &(g->g_nodes.list[nodeID].insertion_edges);
|
||
edgeID = getEdge(g, new_edge, edge_length - i, bases[i]);
|
||
if(edgeID == -1)
|
||
{
|
||
return -1;
|
||
}
|
||
}
|
||
/****************************may have bugs********************************/
|
||
return return_edgeID;
|
||
/****************************may have bugs********************************/
|
||
}
|
||
|
||
|
||
|
||
inline int create_insertion_Edges(Graph* g, long long alignNodeID, uint64_t edge_length, char* bases)
|
||
{
|
||
long long i = 0;
|
||
long long nodeID;
|
||
///should link back to the intial node
|
||
///long long backboneID = alignNodeID + 1;
|
||
long long backboneID = alignNodeID;
|
||
|
||
|
||
if (edge_length < 1)
|
||
{
|
||
return -1;
|
||
}
|
||
|
||
|
||
nodeID = add_Node_Graph(g, bases[0]);
|
||
///add the new node to alignNodeID by insertion_edges
|
||
append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, nodeID, 1, edge_length);
|
||
|
||
alignNodeID = nodeID;
|
||
|
||
for (i = 1; i < (long long)edge_length; i++)
|
||
{
|
||
nodeID = add_Node_Graph(g, bases[i]);
|
||
///add the new node to alignNodeID by insertion_edges
|
||
append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, nodeID, 1, edge_length - i);
|
||
alignNodeID = nodeID;
|
||
}
|
||
|
||
append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, backboneID, 1, 0);
|
||
|
||
return 1;
|
||
}
|
||
|
||
|
||
inline void extract_path(Graph* backbone, int debug_node_in_backbone, int path_i, char* pre)
|
||
{
|
||
int step = G_Node(*backbone, debug_node_in_backbone).insertion_edges.list[path_i].length;
|
||
int string_i = 0, preNode = 0, j = 0;
|
||
if(step != 0)
|
||
{
|
||
string_i = 0;
|
||
preNode = G_Node(*backbone, debug_node_in_backbone).insertion_edges.list[path_i].out_node;
|
||
|
||
for (j = 0; j < step; j++)
|
||
{
|
||
pre[string_i++] = G_Node(*backbone, preNode).base;
|
||
preNode = G_Node(*backbone, preNode).insertion_edges.list[0].out_node;
|
||
}
|
||
}
|
||
|
||
pre[string_i] = '\0';
|
||
}
|
||
|
||
|
||
|
||
inline int get_insertion_Edges_new(Graph* backbone, int debug_node_in_backbone, uint64_t edge_length, char* bases)
|
||
{
|
||
int path_i, j, step, preNode;
|
||
|
||
for (path_i = 0; path_i < (long long)G_Node(*backbone, debug_node_in_backbone).insertion_edges.length; path_i++)
|
||
{
|
||
step = G_Node(*backbone, debug_node_in_backbone).insertion_edges.list[path_i].length;
|
||
|
||
|
||
if(step != (long long)edge_length)
|
||
{
|
||
continue;
|
||
}
|
||
|
||
|
||
if(step != 0)
|
||
{
|
||
preNode = G_Node(*backbone, debug_node_in_backbone).insertion_edges.list[path_i].out_node;
|
||
|
||
for (j = 0; j < step; j++)
|
||
{
|
||
if(G_Node(*backbone, preNode).base != bases[j])
|
||
{
|
||
break;
|
||
}
|
||
|
||
preNode = G_Node(*backbone, preNode).insertion_edges.list[0].out_node;
|
||
}
|
||
|
||
if(j == step)
|
||
{
|
||
return path_i;
|
||
}
|
||
}
|
||
}
|
||
|
||
|
||
return -1;
|
||
}
|
||
|
||
|
||
|
||
|
||
inline void add_insertionEdge_weight(Graph* g, long long alignNodeID, char* insert, long long insert_length)
|
||
{
|
||
|
||
long long nodeID;
|
||
long long edgeID;
|
||
Edge_alloc* edge = &(g->g_nodes.list[alignNodeID].insertion_edges);
|
||
|
||
if (insert_length == 1)
|
||
{
|
||
edgeID = getEdge(g, edge, 1, insert[0]);
|
||
if (edgeID != -1)
|
||
{
|
||
edge->list[edgeID].weight++;
|
||
}
|
||
else ///there is no such edge
|
||
{
|
||
nodeID = add_Node_Graph(g, insert[0]);
|
||
append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
|
||
///add the new node to alignNodeID by insertion_edges
|
||
//should link to the initial node, instead of the next node of the initial node
|
||
///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
|
||
append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
|
||
}
|
||
}
|
||
else
|
||
{
|
||
///edgeID = get_insertion_Edges(g, edge, insert_length, insert);
|
||
edgeID = get_insertion_Edges_new(g, alignNodeID, insert_length, insert);
|
||
if (edgeID != -1)
|
||
{
|
||
///just one outdegree
|
||
edge->list[edgeID].weight++;
|
||
}
|
||
else
|
||
{
|
||
create_insertion_Edges(g, alignNodeID, insert_length, insert);
|
||
}
|
||
}
|
||
}
|
||
|
||
|
||
|
||
#endif |