mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-24 06:18:13 +08:00
fix insertion bug
This commit is contained in:
Haoyu Cheng
+478
-22
@@ -1593,6 +1593,22 @@ inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_IN
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}
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inline void add_base_to_correct_read_directly(Correct_dumy* dumy, char base)
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{
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if (dumy->corrected_read_length + 2 > dumy->corrected_read_size)
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{
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dumy->corrected_read_size = dumy->corrected_read_size * 2;
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dumy->corrected_read = (char*)realloc(dumy->corrected_read, dumy->corrected_read_size);
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}
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dumy->corrected_read[dumy->corrected_read_length] = base;
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dumy->corrected_read_length++;
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dumy->corrected_read[dumy->corrected_read_length] = '\0';
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}
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inline void add_base_to_correct_read(Correct_dumy* dumy, char base, int is_error)
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{
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///deletion就不要管
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@@ -1632,6 +1648,223 @@ inline void add_segment_to_correct_read(Correct_dumy* dumy, char* segment, long
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dumy->corrected_read[dumy->corrected_read_length] = '\0';
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}
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///返回下一个backbone节点上的ID
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long long inline add_path_to_correct_read(Graph* backbone, Correct_dumy* dumy, long long currentNodeID,
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long long type, long long edgeID)
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{
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//long long i;
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long long nodeID;
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///包括匹配和误配两种情况
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if (type == MISMATCH)
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{
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///这是match的情况
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if(backbone->g_nodes.list[currentNodeID].mismatch_edges.list[edgeID].length == 0)
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{
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nodeID = backbone->g_nodes.list[currentNodeID].mismatch_edges.list[edgeID].out_node;
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add_base_to_correct_read_directly(dumy, backbone->g_nodes.list[nodeID].base);
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///match所以dumy->corrected_base不要+1
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/***********需要注释掉********* */
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if (nodeID != currentNodeID + 1)
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{
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fprintf(stderr, "error match\n");
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}
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/***********需要注释掉********* */
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return nodeID;
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}
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else ///这是mismatch的情况
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{
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nodeID = backbone->g_nodes.list[currentNodeID].mismatch_edges.list[edgeID].out_node;
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add_base_to_correct_read_directly(dumy, backbone->g_nodes.list[nodeID].base);
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dumy->corrected_base++;
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///这种中间节点只有一个元素，所以直接list[0]
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nodeID = backbone->g_nodes.list[nodeID].mismatch_edges.list[0].out_node;
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/***********需要注释掉********* */
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if (nodeID != currentNodeID + 1)
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{
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fprintf(stderr, "error mismatch\n");
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}
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/***********需要注释掉********* */
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return nodeID;
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}
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}
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else if (type == DELETION)
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{
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nodeID = backbone->g_nodes.list[currentNodeID].deletion_edges.list[edgeID].out_node;
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/***********需要注释掉********* */
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if (!(nodeID >= backbone->s_start_nodeID && nodeID <= backbone->s_end_nodeID))
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{
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fprintf(stderr, "error deletion 1\n");
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}
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if (nodeID <= currentNodeID)
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{
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fprintf(stderr, "error deletion 2\n");
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}
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/***********需要注释掉********* */
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dumy->corrected_base += nodeID - currentNodeID;
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return nodeID;
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}
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else if (type == INSERTION)
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{
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///这个一定要变成0
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backbone->g_nodes.list[currentNodeID].num_insertions = 0;
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nodeID = backbone->g_nodes.list[currentNodeID].insertion_edges.list[edgeID].out_node;
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long long step = backbone->g_nodes.list[currentNodeID].insertion_edges.list[edgeID].length;
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long long i;
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for (i = 0; i < step; i++)
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{
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add_base_to_correct_read_directly(dumy, backbone->g_nodes.list[nodeID].base);
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///只有一条边
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nodeID = backbone->g_nodes.list[nodeID].insertion_edges.list[0].out_node;
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}
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dumy->corrected_base += step;
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/***********需要注释掉********* */
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if (nodeID != currentNodeID)
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{
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fprintf(stderr, "error insertion\n");
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}
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/***********需要注释掉********* */
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return nodeID;
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}
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else
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{
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fprintf(stderr, "error type\n");
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}
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}
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void get_seq_from_Graph(Graph* backbone, Correct_dumy* dumy)
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{
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long long new_seq_length = 0;
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long long currentNodeID;
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long long i;
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// 总共有以下几种情况:
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// 1. match 2. mismatch (A, C, G, T, N) 3. deletion 4. insertion (A, C, G, T)
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// 其实就是 1. 自己本身的weight 2. alignToNode的weight 3. insertion节点的weight
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long long max_count;
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int max_type;
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long long max_edge;
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long long total_count;
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long long nodeID;
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char current_base;
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long long current_weight;
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currentNodeID = backbone->s_start_nodeID;
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while (currentNodeID != backbone->s_end_nodeID)
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{
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total_count = 0;
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max_count = -1;
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max_type = -1;
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max_edge = -1;
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///假如这是个backbone节点
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///有三类出边
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///1. mismatch_edges 2. insertion_edges 3. deletion_edges
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if (currentNodeID >= backbone->s_start_nodeID && currentNodeID <= backbone->s_end_nodeID)
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{
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///mismatch_edges
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].mismatch_edges.length; i++)
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{
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if (backbone->g_nodes.list[currentNodeID].num_insertions != 0)
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{
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current_weight = backbone->g_nodes.list[currentNodeID].mismatch_edges.list[i].weight -
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backbone->g_nodes.list[currentNodeID].mismatch_edges.list[i].num_insertions;
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}
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else
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{
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current_weight = backbone->g_nodes.list[currentNodeID].mismatch_edges.list[i].weight;
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}
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total_count = total_count + current_weight;
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///match
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///match要处理插入的情况
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///如果这里有insertion, 这个节点会过两遍
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///第一遍num_insertions > 0, 第二遍num_insertions=0
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if (current_weight > max_count)
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{
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max_count = current_weight;
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max_edge = i;
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max_type = MISMATCH;
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}
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}
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///insertion_edges
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if (backbone->g_nodes.list[currentNodeID].num_insertions != 0)
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{
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].insertion_edges.length; i++)
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{
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total_count = total_count + backbone->g_nodes.list[currentNodeID].insertion_edges.list[i].weight;
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if (backbone->g_nodes.list[currentNodeID].insertion_edges.list[i].weight > max_count)
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{
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max_count = backbone->g_nodes.list[currentNodeID].insertion_edges.list[i].weight;
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max_edge = i;
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max_type = INSERTION;
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}
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}
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}
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///deletion_edges
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].deletion_edges.length; i++)
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{
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total_count = total_count + backbone->g_nodes.list[currentNodeID].deletion_edges.list[i].weight;
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if (backbone->g_nodes.list[currentNodeID].deletion_edges.list[i].weight > max_count)
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{
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max_count = backbone->g_nodes.list[currentNodeID].deletion_edges.list[i].weight;
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max_edge = i;
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max_type = DELETION;
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}
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}
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///这种情况下矫正
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if(max_count >= total_count*CORRECT_THRESHOLD)
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{
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currentNodeID = add_path_to_correct_read(backbone, dumy, currentNodeID, max_type, max_edge);
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}
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else ///不矫正, 直接取下一个backbone节点
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{
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currentNodeID++;
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add_base_to_correct_read_directly(dumy, backbone->g_nodes.list[currentNodeID].base);
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}
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///fprintf(stderr, "currentNodeID: %d, max_type: %d\n", currentNodeID, max_type);
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}
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else ///非backbone节点就会出错了
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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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///从backbone_start遍历到backbone_end节点，生成出来的seq要接着放到dumy->corrected_read中
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void get_seq_from_Graph(Graph* backbone, long long backbone_start, long long backbone_end, Correct_dumy* dumy)
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{
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@@ -1836,9 +2069,232 @@ void get_seq_from_Graph(Graph* backbone, long long backbone_start, long long bac
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add_base_to_correct_read(dumy, current_base, max_type);
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}
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**/
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/**
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///从backbone_start遍历到backbone_end节点，生成出来的seq要接着放到dumy->corrected_read中
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void get_seq_from_Graph_Len2(Graph* backbone, long long backbone_start, long long backbone_end, Correct_dumy* dumy)
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{
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long long new_seq_length = 0;
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long long currentNodeID;
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long long i;
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// 总共有以下几种情况:
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// 1. match 2. mismatch (A, C, G, T, N) 3. deletion 4. insertion (A, C, G, T)
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// 其实就是 1. 自己本身的weight 2. alignToNode的weight 3. insertion节点的weight
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long long max_count;
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int max_type;
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long long max_node;
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long long total_count;
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long long nodeID;
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char current_base;
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char buffer[2];
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currentNodeID = backbone_start;
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while (currentNodeID != backbone_end)
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{
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total_count = 0;
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max_count = -1;
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///图上能够被遍历到的有两种节点
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///1. backbone节点 2. insertion节点
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///backbone节点才有match/mismatch/deletion
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///insertion这些都没有，就是无脑看出边
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///假如这是个backbone节点
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if (currentNodeID >= backbone_start && currentNodeID <= backbone_end)
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{
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///match
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total_count += backbone->g_nodes.list[currentNodeID].weight;
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max_count = backbone->g_nodes.list[currentNodeID].weight;
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max_type = 0;
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max_node = currentNodeID;
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///mismatch和deletion (A, C, G, T, N, D, 除了自己的那个字符)
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].alignedTo_Nodes.length; i++)
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{
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nodeID = backbone->g_nodes.list[currentNodeID].alignedTo_Nodes.list[i].out_node;
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total_count += backbone->g_nodes.list[nodeID].weight;
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if (backbone->g_nodes.list[nodeID].weight > max_count)
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{
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max_count = backbone->g_nodes.list[nodeID].weight;
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max_type = 1;
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max_node = nodeID;
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}
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}
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///insertion (A, C, G, T, N)
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///注意这个出边还得避开下一个backbone节点
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].outcome_edges.length; i++)
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{
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if (backbone->g_nodes.list[currentNodeID].outcome_edges.list[i].weight == 2)
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{
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///fprintf(stderr, "error\n");
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nodeID = backbone->g_nodes.list[currentNodeID].outcome_edges.list[i].out_node;
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total_count += backbone->g_nodes.list[nodeID].weight;
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if (backbone->g_nodes.list[nodeID].weight > max_count)
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{
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max_count = backbone->g_nodes.list[nodeID].weight;
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max_type = 2;
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max_node = nodeID;
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}
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///拿到的nodeID应该一定不是backbone上的，如果是就错了
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if (nodeID >= backbone_start && nodeID <= backbone_end)
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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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else ///如果是insertion节点，就无脑看出边
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{
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if (backbone->g_nodes.list[currentNodeID].outcome_edges.length!=1)
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{
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fprintf(stderr, "error000\n");
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}
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///insertion (A, C, G, T, N)
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///注意这个出边不用避开下一个backbone节点
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].outcome_edges.length; i++)
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{
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if (backbone->g_nodes.list[currentNodeID].outcome_edges.list[i].weight == 2)
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{
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nodeID = backbone->g_nodes.list[currentNodeID].outcome_edges.list[i].out_node;
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total_count += backbone->g_nodes.list[nodeID].weight;
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if (backbone->g_nodes.list[nodeID].weight > max_count)
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{
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max_count = backbone->g_nodes.list[nodeID].weight;
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max_type = 2;
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max_node = nodeID;
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}
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}
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else ///如果边不是2就不对了
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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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if(max_count >= total_count*CORRECT_THRESHOLD)
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{
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current_base = backbone->g_nodes.list[max_node].base;
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///说明是insertion
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if (max_type == 2)
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{
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currentNodeID = max_node;
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}
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else ///其他情况依然沿着backbone向前
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{
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currentNodeID++;
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}
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}
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else
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{
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///假如这是个backbone节点, 不矫正
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if (currentNodeID >= backbone_start && currentNodeID <= backbone_end)
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{
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current_base = backbone->g_nodes.list[currentNodeID].base;
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currentNodeID++;
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} ///应该不存在这个问题
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else///如果在insertion节点上不达标很麻烦...,只能选最大的了
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{
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///因为现在每个insert节点只有一个出边，且这个出边到backbone
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fprintf(stderr, "error111\n");
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}
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}
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if (max_count <= 0)
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{
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fprintf(stderr, "error\n");
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}
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if (current_base < 'A')
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{
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buffer[0] = s_H[(current_base >> 2) & ((uint8_t)3)];
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buffer[1] = s_H[current_base & ((uint8_t)3)];
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add_base_to_correct_read(dumy, buffer[0], max_type);
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add_base_to_correct_read(dumy, buffer[1], max_type);
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}
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else
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{
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add_base_to_correct_read(dumy, current_base, max_type);
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}
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}
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///最后还要处理backbone_end这个节点
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total_count = 0;
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max_count = -1;
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///这个节点肯定是backbone上的节点啊
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///match
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total_count += backbone->g_nodes.list[currentNodeID].weight;
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max_count = backbone->g_nodes.list[currentNodeID].weight;
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max_type = 0;
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max_node = currentNodeID;
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///mismatch和deletion (A, C, G, T, N, D, 除了自己的那个字符)
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for (i = 0; i < backbone->g_nodes.list[currentNodeID].alignedTo_Nodes.length; i++)
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{
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nodeID = backbone->g_nodes.list[currentNodeID].alignedTo_Nodes.list[i].out_node;
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total_count += backbone->g_nodes.list[nodeID].weight;
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if (backbone->g_nodes.list[nodeID].weight > max_count)
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{
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max_count = backbone->g_nodes.list[nodeID].weight;
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max_type = 1;
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max_node = nodeID;
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}
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}
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///这个节点不应该有任何出边了
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if(backbone->g_nodes.list[currentNodeID].outcome_edges.length)
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{
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fprintf(stderr, "haha\n");
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}
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if(max_count >= total_count*CORRECT_THRESHOLD)
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||||
{
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current_base = backbone->g_nodes.list[max_node].base;
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||||
}
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||||
else
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||||
{
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current_base = backbone->g_nodes.list[currentNodeID].base;
|
||||
}
|
||||
|
||||
|
||||
if (max_count <= 0)
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
|
||||
add_base_to_correct_read(dumy, current_base, max_type);
|
||||
|
||||
}
|
||||
**/
|
||||
|
||||
|
||||
void window_consensus(char* r_string, long long window_start, long long window_end,
|
||||
overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, Graph* g)
|
||||
{
|
||||
@@ -1902,31 +2358,19 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, Graph*
|
||||
y_string, y_length, &(overlap_list->list[overlapID].w_list[windowID].cigar), startNodeID, endNodeID);
|
||||
}
|
||||
|
||||
get_seq_from_Graph(g, dumy);
|
||||
|
||||
get_seq_from_Graph(g, startNodeID, endNodeID, dumy);
|
||||
|
||||
///get_seq_from_Graph(g, startNodeID, endNodeID, dumy);
|
||||
///get_seq_from_Graph_Len2(g, startNodeID, endNodeID, dumy);
|
||||
|
||||
|
||||
|
||||
///debug_graph(g, backbone_length);
|
||||
|
||||
|
||||
|
||||
/**
|
||||
if (startNodeID != 0 || endNodeID != backbone_length - 1)
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
|
||||
|
||||
for (i = startNodeID; i <= backbone_length; i++)
|
||||
{
|
||||
if(g->g_nodes.list[i].alignedTo_Nodes.length > 5)
|
||||
{
|
||||
fprintf(stderr, "error 1\n");
|
||||
}
|
||||
|
||||
if(g->g_nodes.list[i].outcome_edges.length > 4)
|
||||
{
|
||||
fprintf(stderr, "error 2\n");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
for (i = 0; i < dumy->length; i++)
|
||||
{
|
||||
///这个是那个overlap的ID，而不是overlap里对应窗口的ID
|
||||
@@ -2160,11 +2604,14 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
generate_consensus(overlap_list, R_INF, g_read, dumy, g);
|
||||
|
||||
|
||||
///fprintf(stderr, "length: %lld, corrected_base: %lld\n", g_read->length, dumy->corrected_base);
|
||||
/**
|
||||
///fprintf(stderr, "length: %lld, corrected_base: %lld\n", g_read->length, dumy->corrected_base);
|
||||
|
||||
EdlibAlignResult result = edlibAlign(g_read->seq, g_read->length, dumy->corrected_read, dumy->corrected_read_length,
|
||||
edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_PATH, NULL, 0));
|
||||
|
||||
|
||||
|
||||
if (result.status == EDLIB_STATUS_OK) {
|
||||
if (dumy->corrected_base == 0 && result.editDistance!= 0)
|
||||
{
|
||||
@@ -2193,6 +2640,15 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
}
|
||||
|
||||
edlibFreeAlignResult(result);
|
||||
|
||||
for (i = 0; i < dumy->corrected_read_length; i++)
|
||||
{
|
||||
if (dumy->corrected_read[i] != 'A' && dumy->corrected_read[i] != 'C' && dumy->corrected_read[i] != 'G' && dumy->corrected_read[i] != 'T')
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
|
||||
}
|
||||
**/
|
||||
|
||||
/************需要注释掉********* */
|
||||
|
||||
Reference in New Issue
Block a user