mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
621 lines
16 KiB
C++
621 lines
16 KiB
C++
#include "POA.h"
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#include <stdlib.h>
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#include "Correct.h"
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#include "Process_Read.h"
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#define INIT_EDGE_SIZE 50
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#define INCREASE_EDGE_SIZE 5
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#define INIT_NODE_SIZE 16000
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void init_Edge_alloc(Edge_alloc* list)
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{
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if (list->list == NULL)
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{
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list->size = INIT_EDGE_SIZE;
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list->length = 0;
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list->list = (Edge*)malloc(sizeof(Edge)*list->size);
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}
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else
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{
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list->length = 0;
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}
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}
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void clear_Edge_alloc(Edge_alloc* list)
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{
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list->length = 0;
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}
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void destory_Edge_alloc(Edge_alloc* list)
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{
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free(list->list);
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}
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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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{
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if (list->length + 1 > list->size)
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{
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list->size = list->size + INCREASE_EDGE_SIZE;
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list->list = (Edge*)realloc(list->list, sizeof(Edge)*list->size);
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}
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list->list[list->length].in_node = in_node;
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list->list[list->length].out_node = out_node;
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list->list[list->length].weight = weight;
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list->list[list->length].length = length;
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list->list[list->length].num_insertions = 0;
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list->length++;
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}
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void init_Node_alloc(Node_alloc* list)
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{
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list->size = INIT_NODE_SIZE;
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list->length = 0;
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list->list = (Node*)malloc(sizeof(Node)*list->size);
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list->sort.size = 0;
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list->sort.list = NULL;
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list->sort.visit = NULL;
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list->sort.iterative_buffer = NULL;
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list->sort.iterative_buffer_visit = NULL;
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long long i;
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for (i = 0; i < list->size; i++)
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{
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list->list[i].insertion_edges.list=NULL;
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list->list[i].mismatch_edges.list=NULL;
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list->list[i].deletion_edges.list=NULL;
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}
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}
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void destory_Node_alloc(Node_alloc* list)
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{
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uint64_t i =0;
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for (i = 0; i < list->length; i++)
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{
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destory_Edge_alloc(&list->list[i].deletion_edges);
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destory_Edge_alloc(&list->list[i].insertion_edges);
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destory_Edge_alloc(&list->list[i].mismatch_edges);
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}
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free(list->list);
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free(list->sort.list);
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free(list->sort.visit);
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free(list->sort.iterative_buffer);
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free(list->sort.iterative_buffer_visit);
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///free(list->topo_order);
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}
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void clear_Node_alloc(Node_alloc* list)
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{
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uint64_t i =0;
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for (i = 0; i < list->length; i++)
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{
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clear_Edge_alloc(&list->list[i].insertion_edges);
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clear_Edge_alloc(&list->list[i].mismatch_edges);
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clear_Edge_alloc(&list->list[i].deletion_edges);
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}
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list->length = 0;
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}
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uint64_t append_Node_alloc(Node_alloc* list, char base)
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{
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if (list->length + 1 > list->size)
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{
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long long i = list->size;
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///list->topo_order这里用不到，所以不用先分配空间
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///但是还是一起分配了吧，免得麻烦
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list->size = list->size * 2;
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list->list = (Node*)realloc(list->list, sizeof(Node)*list->size);
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///list->topo_order = (uint64_t*)realloc(list->topo_order, sizeof(uint64_t)*list->size);
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for (; i < list->size; i++)
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{
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list->list[i].deletion_edges.list=NULL;
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list->list[i].insertion_edges.list=NULL;
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list->list[i].mismatch_edges.list=NULL;
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}
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}
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list->list[list->length].ID = list->length;
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list->list[list->length].base = base;
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list->list[list->length].weight = 1;
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list->list[list->length].num_insertions = 0;
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init_Edge_alloc(&list->list[list->length].deletion_edges);
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init_Edge_alloc(&list->list[list->length].insertion_edges);
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init_Edge_alloc(&list->list[list->length].mismatch_edges);
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list->length++;
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return list->length - 1;
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}
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void init_Graph(Graph* g)
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{
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init_Node_alloc(&g->g_nodes);
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g->g_n_edges = 0;
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g->g_n_nodes = 0;
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g->g_next_nodeID = 0;
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g->s_end_nodeID = 0;
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g->s_start_nodeID = 0;
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g->seq = NULL;
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g->seqID = (uint64_t)-1;
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}
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void destory_Graph(Graph* g)
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{
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destory_Node_alloc(&g->g_nodes);
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}
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void clear_Graph(Graph* g)
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{
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clear_Node_alloc(&g->g_nodes);
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g->g_n_edges = 0;
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g->g_n_nodes = 0;
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g->g_next_nodeID = 0;
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g->s_end_nodeID = 0;
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g->s_start_nodeID = 0;
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g->seq = NULL;
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g->seqID = (uint64_t)-1;
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}
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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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{
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long long firstID, lastID, nodeID, i;
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firstID = -1;
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lastID = -1;
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if(g_read_length == 0)
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return;
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///start node
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nodeID = add_Node_Graph(g, 'S');
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firstID = nodeID;
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lastID = nodeID;
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for (i = 0; i < g_read_length; i++)
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{
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nodeID = add_Node_Graph(g, g_read_seq[i]);
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////fprintf(stderr, "nodeID: %llu\n", nodeID);
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if (firstID == -1)
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{
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firstID = nodeID;
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}
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if (lastID != -1)
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{
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/**
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///0是match边
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add_Edge_Graph(g, lastID, nodeID, 0);
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**/
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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(&(g->g_nodes.list[lastID].mismatch_edges), lastID, nodeID, 1, 0);
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}
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lastID = nodeID;
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}
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*startID = firstID;
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*endID = lastID;
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g->s_start_nodeID = firstID;
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g->s_end_nodeID = lastID;
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}
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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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{
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int x_i, y_i, cigar_i;
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x_i = 0;
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y_i = 0;
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cigar_i = 0;
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int operation;
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int operationLen;
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int i;
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int last_operation = -1;
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///note that node 0 is the start node
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///0 is match, 1 is mismatch, 2 is up, 3 is left
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///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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while (cigar_i < cigar->length)
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{
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operation = cigar->C_C[cigar_i];
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operationLen = cigar->C_L[cigar_i];
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///这种情况代表匹配和mismatch
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if (operation == 0 || operation == 1)
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{
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for (i = 0; i < operationLen; i++)
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{
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//backbone->g_nodes.list[currentNodeID].weight++;
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///前面是插入，后面有可能是误配，也有可能是匹配
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add_mismatchEdge_weight(backbone, currentNodeID, y_string[y_i], last_operation);
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x_i++;
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y_i++;
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currentNodeID++;
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}
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}///insertion
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else if (operation == 2)
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{
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///cigar的起始和结尾不可能是2，所以这里-1没问题
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///if (operationLen <= CORRECT_INDEL_LENGTH)
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{
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add_insertionEdge_weight(backbone, currentNodeID, y_string + y_i, operationLen);
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backbone->g_nodes.list[currentNodeID].num_insertions++;
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}
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y_i += operationLen;
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}
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else if (operation == 3)
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{
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///3是y缺字符（x多字符），也就是backbone多字符
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///这个相当于在backbone对应字符处变成了‘——’
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///因此可以用mismatch类似的方法处理
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///if (operationLen <= CORRECT_INDEL_LENGTH)
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{
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///add_deletion_to_backbone(backbone, ¤tNodeID, operationLen);
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///在编辑距离中，前面是个插入，后面是个删除，这种情况是不存在的
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///为了保险要不还给他加上吧
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///先不加
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add_deletionEdge_weight(backbone, currentNodeID, operationLen);
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}
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currentNodeID += operationLen;
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x_i += operationLen;
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}
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last_operation = operation;
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cigar_i++;
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}
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/**
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///cigar的起始和结尾不可能是2
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if (cigar->C_C[0] == 2 || cigar->C_C[cigar->length - 1] == 2)
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{
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fprintf(stderr, "error\n");
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}
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if (x_i != x_length)
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{
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fprintf(stderr, "x_i: %d, x_length: %d\n", x_i, x_length);
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}
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if (y_i != y_length)
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{
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fprintf(stderr, "y_i: %d, y_length: %d\n", y_i, y_length);
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}
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**/
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}
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void debug_graph(Graph* g, long long backbone_length)
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{
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long long i = 0;
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if (g->s_start_nodeID != 0 || g->s_end_nodeID != backbone_length)
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{
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fprintf(stderr, "error\n");
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}
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for (i = g->s_start_nodeID; i <= g->s_end_nodeID; i++)
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{
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if(g->g_nodes.list[i].weight != 1)
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{
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fprintf(stderr, "error node weight\n");
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}
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if(g->g_nodes.list[i].mismatch_edges.length > 4)
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{
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fprintf(stderr, "error mismatch_edges\n");
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}
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if(g->g_nodes.list[i].mismatch_edges.length < 1 && i != g->s_end_nodeID)
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{
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fprintf(stderr, "i: %d, error mismatch_edges: %d\n", i, g->g_nodes.list[i].mismatch_edges.length);
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}
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}
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for (i = 0; i < g->g_nodes.length; i++)
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{
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if(g->g_nodes.list[i].ID < g->s_start_nodeID || g->g_nodes.list[i].ID > g->s_end_nodeID)
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{
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if (g->g_nodes.list[i].deletion_edges.length +
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g->g_nodes.list[i].insertion_edges.length +
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g->g_nodes.list[i].mismatch_edges.length
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!= 1)
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{
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fprintf(stderr, "g->s_start_nodeID: %lld\n",
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g->s_start_nodeID);
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fprintf(stderr, "g->s_end_nodeID: %lld\n",
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g->s_end_nodeID);
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fprintf(stderr, "deletion_edges_length: %lld\n",
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g->g_nodes.list[i].deletion_edges.length);
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fprintf(stderr, "insertion_edges_length: %lld, \n",
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g->g_nodes.list[i].insertion_edges.length);
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fprintf(stderr, "g->g_nodes.list[i].insertion_edges.list[0].length: %lld, \n",
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g->g_nodes.list[i].insertion_edges.list[0].length);
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fprintf(stderr, "g->g_nodes.list[i].insertion_edges.list[1].length: %lld, \n",
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g->g_nodes.list[i].insertion_edges.list[1].length);
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fprintf(stderr, "mismatch_edges_length: %lld\n",
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g->g_nodes.list[i].mismatch_edges.length);
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}
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else
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{
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///不是0肯定是1
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if (g->g_nodes.list[i].deletion_edges.length != 0)
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{
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long long step = g->g_nodes.list[i].deletion_edges.list[0].length;
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long long nodeID = i;
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for (int j = 0; j < step; j++)
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{
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nodeID = g->g_nodes.list[nodeID].deletion_edges.list[0].out_node;
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}
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nodeID = g->g_nodes.list[nodeID].deletion_edges.list[0].out_node;
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if (nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID)
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{
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fprintf(stderr, "error\n");
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}
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}
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if (g->g_nodes.list[i].insertion_edges.length != 0)
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{
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long long step = g->g_nodes.list[i].insertion_edges.list[0].length;
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long long nodeID = i;
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for (int j = 0; j < step; j++)
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{
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nodeID = g->g_nodes.list[nodeID].insertion_edges.list[0].out_node;
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}
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nodeID = g->g_nodes.list[nodeID].insertion_edges.list[0].out_node;
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if ((nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID))
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{
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fprintf(stderr, "error: step: %d\n", step);
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}
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}
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if (g->g_nodes.list[i].mismatch_edges.length != 0)
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{
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long long step = g->g_nodes.list[i].mismatch_edges.list[0].length;
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long long nodeID = i;
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for (int j = 0; j < step; j++)
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{
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nodeID = g->g_nodes.list[nodeID].mismatch_edges.list[0].out_node;
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}
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nodeID = g->g_nodes.list[nodeID].mismatch_edges.list[0].out_node;
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if (nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID)
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{
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fprintf(stderr, "error\n");
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}
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}
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}
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}
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}
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}
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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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{
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/**
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int x_i, y_i, cigar_i;
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x_i = 0;
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y_i = 0;
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cigar_i = 0;
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int operation;
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int operationLen;
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int i;
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///0 is match, 1 is mismatch, 2 is up, 3 is left
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///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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///while (x_i < x_len && y_i < y_len && cigar_i < cigar->length)
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while (cigar_i < cigar->length)
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{
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operation = cigar->C_C[cigar_i];
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operationLen = cigar->C_L[cigar_i];
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///这种情况代表匹配
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if (operation == 0)
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{
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for (i = 0; i < operationLen; i++)
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{
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if (backbone->g_nodes.list[currentNodeID].base != y_string[y_i])
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{
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fprintf(stderr, "error match\n");
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}
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backbone->g_nodes.list[currentNodeID].weight--;
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x_i++;
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y_i++;
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currentNodeID++;
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}
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}
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else if (operation == 1)
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{
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for (i = 0; i < operationLen; i++)
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{
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if (backbone->g_nodes.list[currentNodeID].base == y_string[y_i])
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{
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fprintf(stderr, "error mismatch 1\n");
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}
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long long mismatchID = get_alignToNode(backbone, currentNodeID, y_string[y_i]);
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if(mismatchID == -1)
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{
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fprintf(stderr, "error mismatch 2\n");
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}
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else
|
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{
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backbone->g_nodes.list[mismatchID].weight--;
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}
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x_i++;
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y_i++;
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currentNodeID++;
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}
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}
|
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else if (operation == 2)
|
||
{
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long long nodeID = currentNodeID - 1;
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long long mismatchID;
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|
||
for (i = 0; i < operationLen; i++)
|
||
{
|
||
mismatchID = get_insertion_Node(backbone, nodeID, y_string[y_i]);
|
||
|
||
if (mismatchID == -1)
|
||
{
|
||
fprintf(stderr, "error insertion 1, i: %d\n", i);
|
||
}
|
||
else
|
||
{
|
||
backbone->g_nodes.list[mismatchID].weight--;
|
||
}
|
||
|
||
nodeID = mismatchID;
|
||
|
||
y_i++;
|
||
}
|
||
///注意这里是x_string[x_i]而不是x_string[currentNodeID]
|
||
mismatchID = get_insertion_Node(backbone, nodeID, x_string[x_i]);
|
||
if (mismatchID == -1)
|
||
{
|
||
fprintf(stderr, "error insertion 2, i: %d, x_i: %d\n", i, x_i);
|
||
}
|
||
|
||
|
||
if (mismatchID != currentNodeID)
|
||
{
|
||
fprintf(stderr, "error insertion 3, i: mismatchID: %d, currentNodeID: %d\n", mismatchID, currentNodeID);
|
||
}
|
||
|
||
|
||
|
||
|
||
}
|
||
else if (operation == 3)
|
||
{
|
||
for (i = 0; i < operationLen; i++)
|
||
{
|
||
|
||
long long mismatchID = get_alignToNode(backbone, currentNodeID, 'D');
|
||
|
||
if(mismatchID == -1)
|
||
{
|
||
fprintf(stderr, "error deletion 2\n");
|
||
}
|
||
else
|
||
{
|
||
backbone->g_nodes.list[mismatchID].weight--;
|
||
}
|
||
|
||
x_i++;
|
||
currentNodeID++;
|
||
}
|
||
}
|
||
|
||
cigar_i++;
|
||
}
|
||
|
||
|
||
if (cigar->C_C[0] == 2 || cigar->C_C[cigar->length - 1] == 2)
|
||
{
|
||
fprintf(stderr, "error\n");
|
||
}
|
||
|
||
|
||
if (x_i != x_length)
|
||
{
|
||
fprintf(stderr, "x_i: %d, x_length: %d\n", x_i, x_length);
|
||
}
|
||
|
||
if (y_i != y_length)
|
||
{
|
||
fprintf(stderr, "y_i: %d, y_length: %d\n", y_i, y_length);
|
||
}
|
||
**/
|
||
|
||
}
|
||
|
||
|
||
|
||
|