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112 lines
2.9 KiB
C
112 lines
2.9 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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} 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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char base;
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Edge_alloc income_edges;
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Edge_alloc outcome_edges;
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Edge_alloc alignedTo_Nodes;
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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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Node total_start;
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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);
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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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#endif |