mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
411 lines
12 KiB
C
411 lines
12 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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/**
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1. 单个节点信息
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(1) ID
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(2) base
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(3) 入边信息
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(4) 出边信息
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(5) 比对到什么节点
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2. 各个节点信息，用数组下标组织，数组下标就是节点ID; 还要存拓扑排序后的下标和节点ID的对应关系
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3. 边
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(1) 边的起始
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(2) 边的结束节点
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(3) 过这条边的序列的label，也就是名称
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4. 各个序列信息
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(1) 这个序列本身
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(2) 这个序列的name或者ID
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(3) 这个序列的在图中对应的起始和结束节点ID
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5. 有两个回溯矩阵，一个是graph的，一个是seq的
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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是match，1是mismatch，2是x缺字符（y多字符），而3是y缺字符（x多字符）
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uint64_t weight;
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uint64_t num_insertions;
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///这条路径上到backbone节点之前总共有多少节点
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uint64_t length;
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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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} Edge_alloc;
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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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///记录的是以当前节点为尾的deletion个数
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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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} 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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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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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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void Graph_debug(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 debug_graph(Graph* g, long long backbone_length);
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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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///仅仅用于误配边
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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 < 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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///如果上一个操作是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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///说明不存在这么一条边
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if (i == edge->length)
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{
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nodeID = add_Node_Graph(g, base);
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///只有match边长度是0
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///mismatch边长度都是1
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append_Edge_alloc(edge, in_node, nodeID, 1, 1);
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///如果上一个操作是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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///将新节点的mismatch_edges连到backbone上
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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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///获得节点的mismatch_edges长度为1，其他均为0
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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 < 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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///说明不存在这么一条边
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if (i == 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)
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{
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if (deletion_length == 1)
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{
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add_single_deletionEdge_weight(g, alignNodeID, alignNodeID + 1, 0);
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}
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else if (deletion_length == 2)
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{
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add_single_deletionEdge_weight(g, alignNodeID, alignNodeID + 1, 0);
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add_single_deletionEdge_weight(g, alignNodeID, alignNodeID + 2, 0);
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add_single_deletionEdge_weight(g, alignNodeID + 1, alignNodeID + 2, 0);
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}
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else if (deletion_length > 2)
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{
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///fprintf(stderr, "too long deletion!\n");
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add_single_deletionEdge_weight(g, alignNodeID, alignNodeID + deletion_length, 0);
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}
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}
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inline int getEdge(Graph* g, Edge_alloc* edge, uint64_t edge_length, char base)
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{
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long long i = 0;
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long long nodeID;
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for (i = 0; i < edge->length; i++)
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{
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if (edge->list[i].length == edge_length)
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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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return i;
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}
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}
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}
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return -1;
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}
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inline int get_insertion_Edges(Graph* g, Edge_alloc* edge, uint64_t edge_length, char* bases)
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{
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long long i = 0;
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long long nodeID;
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long long edgeID;
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if (edge_length < 1)
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{
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return -1;
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}
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edgeID = getEdge(g, edge, edge_length, bases[0]);
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long long return_edgeID = edgeID;
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if(edgeID == -1)
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{
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return -1;
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}
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Edge_alloc* new_edge = edge;
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for (i = 1; i < edge_length; i++)
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{
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nodeID = new_edge->list[edgeID].out_node;
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new_edge = &(g->g_nodes.list[nodeID].insertion_edges);
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edgeID = getEdge(g, new_edge, edge_length - i, bases[i]);
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if(edgeID == -1)
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{
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return -1;
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}
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}
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return edgeID;
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}
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inline int create_insertion_Edges(Graph* g, long long alignNodeID, uint64_t edge_length, char* bases)
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{
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long long i = 0;
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long long nodeID;
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///最后应该连回原节点
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///long long backboneID = alignNodeID + 1;
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long long backboneID = alignNodeID;
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if (edge_length < 1)
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{
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return -1;
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}
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nodeID = add_Node_Graph(g, bases[0]);
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///将新加入的节点通过insertion_edges接到alignNodeID上
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append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, nodeID, 1, edge_length);
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alignNodeID = nodeID;
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for (i = 1; i < edge_length; i++)
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{
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nodeID = add_Node_Graph(g, bases[i]);
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///将新加入的节点通过insertion_edges接到alignNodeID上
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append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, nodeID, 1, edge_length - i);
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alignNodeID = nodeID;
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}
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append_Edge_alloc(&(g->g_nodes.list[alignNodeID].insertion_edges), alignNodeID, backboneID, 1, 0);
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}
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inline void add_insertionEdge_weight(Graph* g, long long alignNodeID, char* insert, long long insert_length)
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{
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long long i = 0;
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long long nodeID;
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long long edgeID;
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Edge_alloc* edge = &(g->g_nodes.list[alignNodeID].insertion_edges);
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if (insert_length == 1)
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{
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edgeID = getEdge(g, edge, 1, insert[0]);
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if (edgeID != -1)
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{
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///这条路均只有一个出度
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edge->list[edgeID].weight++;
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}
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else ///不存在这么一条边
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{
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nodeID = add_Node_Graph(g, insert[0]);
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append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
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///将新加入的节点通过insertion_edges接回backbone上
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///应该连回到原节点，而不是原节点的下一个节点
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///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
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append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
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}
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}
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else if (insert_length == 2)
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{
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/*******************第0个字符********************* */
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edgeID = getEdge(g, edge, 1, insert[0]);
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if (edgeID != -1)
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{
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///这条路均只有一个出度
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edge->list[edgeID].weight++;
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}
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else ///不存在这么一条边
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{
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nodeID = add_Node_Graph(g, insert[0]);
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append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
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///将新加入的节点通过insertion_edges接回backbone上
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///应该连回到原节点，而不是原节点的下一个节点
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///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
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append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
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}
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/*******************第0个字符********************* */
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/*******************第1个字符********************* */
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if (insert[1] != insert[0])
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{
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edgeID = getEdge(g, edge, 1, insert[1]);
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if (edgeID != -1)
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{
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///这条路均只有一个出度
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edge->list[edgeID].weight++;
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}
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else ///不存在这么一条边
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{
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nodeID = add_Node_Graph(g, insert[1]);
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append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
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///将新加入的节点通过insertion_edges接回backbone上
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///应该连回到原节点，而不是原节点的下一个节点
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///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
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append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
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}
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}
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/*******************第1个字符********************* */
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/**********************两个字符******************* */
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edgeID = get_insertion_Edges(g, edge, 2, insert);
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if (edgeID != -1)
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{
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///这条路均只有一个出度
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edge->list[edgeID].weight++;
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}
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else
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{
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create_insertion_Edges(g, alignNodeID, insert_length, insert);
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}
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/**********************两个字符******************* */
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}
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else if (insert_length > 2)
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{
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////fprintf(stderr, "too long insertion\n");
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/*************************大于2个字符************************** */
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edgeID = get_insertion_Edges(g, edge, insert_length, insert);
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if (edgeID != -1)
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{
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///这条路均只有一个出度
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edge->list[edgeID].weight++;
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}
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else
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{
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create_insertion_Edges(g, alignNodeID, insert_length, insert);
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}
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}
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}
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#endif |