POA

POA.cpp

@@ -0,0 +1,464 @@
+#include "POA.h"
+#include <stdlib.h>
+#define INIT_EDGE_SIZE 50
+#define INCREASE_EDGE_SIZE 5
+#define INIT_NODE_SIZE 16000
+
+
+void check_addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long startID, long long endID)
+{
+    long long reverse_startID, reverse_endID;
+    reverse_startID = startID;
+    reverse_endID = endID;
+    long long i = 0;
+    if (endID - startID + 1 != g_read_length)
+    {
+        fprintf(stderr, "ERROR Length...\n");
+        fprintf(stderr, "startID: %lld, endID: %lld\n", startID, endID);
+        fprintf(stderr, "g_read_length: %lld\n", g_read_length);
+    }
+
+    if (g_read_length == 0)
+    {
+        return;
+    }
+    
+    
+    while (1)
+    {
+        if(g->g_nodes.list[startID].base != g_read_seq[i])
+        {
+            fprintf(stderr, "i: %llu, ERROR Node Base...\n", i);
+
+        }
+
+        if(g->g_nodes.list[startID].outcome_edges.length == 0)
+        {
+            break;
+        }
+
+        startID = g->g_nodes.list[startID].outcome_edges.list[0].out_node;
+
+        i++;
+    }
+
+    if (startID != endID)
+    {
+        fprintf(stderr, "ERROR End Node Base\n");
+    }
+
+
+    i = g_read_length - 1;
+    while (1)
+    {
+        if(g->g_nodes.list[reverse_endID].base != g_read_seq[i])
+        {
+            fprintf(stderr, "i: %llu, g_read_length: %llu, ERROR Node Base...\n", i, g_read_length);
+
+        }
+
+        if(g->g_nodes.list[reverse_endID].income_edges.length == 0)
+        {
+            break;
+        }
+
+        reverse_endID = g->g_nodes.list[reverse_endID].income_edges.list[0].in_node;
+
+        i--;
+    }
+
+    if (reverse_startID != reverse_endID)
+    {
+        fprintf(stderr, "ERROR Start Node Base\n");
+    }
+
+}
+
+
+void init_Edge_alloc(Edge_alloc* list)
+{
+    if (list->list == NULL)
+    {
+        list->size = INIT_EDGE_SIZE;
+        list->length = 0;
+        list->list = (Edge*)malloc(sizeof(Edge)*list->size);
+    }
+    else
+    {
+        list->length = 0;
+    }
+    
+}
+
+void clear_Edge_alloc(Edge_alloc* list)
+{
+    list->length = 0;
+}
+
+void destory_Edge_alloc(Edge_alloc* list)
+{
+    free(list->list);
+}
+
+void append_Edge_alloc(Edge_alloc* list,  uint64_t in_node, uint64_t out_node, uint64_t weight)
+{
+    if (list->length + 1 > list->size)
+    {
+        list->size = list->size + INCREASE_EDGE_SIZE;
+        list->list = (Edge*)realloc(list->list, sizeof(Edge)*list->size);
+    }
+
+    list->list[list->length].in_node = in_node;
+    list->list[list->length].out_node = out_node;
+    list->list[list->length].weight = weight;
+
+    list->length++;
+}
+
+
+
+
+
+
+
+
+void init_Node_alloc(Node_alloc* list)
+{
+    list->size = INIT_NODE_SIZE;
+    list->length = 0;
+    list->list = (Node*)malloc(sizeof(Node)*list->size);
+    list->sort.size = 0;
+    list->sort.list = NULL;
+    list->sort.visit = NULL;
+
+    list->sort.iterative_buffer = NULL;
+    list->sort.iterative_buffer_visit = NULL;
+
+
+    long long i;
+    for (i = 0; i < list->size; i++)
+    {
+        list->list[i].income_edges.list=NULL;
+        list->list[i].outcome_edges.list=NULL;
+        list->list[i].alignedTo_Nodes.list=NULL;
+    }
+    
+}
+
+void destory_Node_alloc(Node_alloc* list)
+{
+    uint64_t i =0;
+    for (i = 0; i < list->length; i++)
+    {
+        destory_Edge_alloc(&list->list[i].income_edges);
+        destory_Edge_alloc(&list->list[i].outcome_edges);
+        destory_Edge_alloc(&list->list[i].alignedTo_Nodes);
+    }
+    free(list->list);
+    free(list->sort.list);
+    free(list->sort.visit);
+    free(list->sort.iterative_buffer);
+    free(list->sort.iterative_buffer_visit);
+    ///free(list->topo_order);
+}
+
+void clear_Node_alloc(Node_alloc* list)
+{
+    uint64_t i =0;
+    for (i = 0; i < list->length; i++)
+    {
+        clear_Edge_alloc(&list->list[i].income_edges);
+        clear_Edge_alloc(&list->list[i].outcome_edges);
+        clear_Edge_alloc(&list->list[i].alignedTo_Nodes);
+    }
+    list->length = 0;
+}
+
+
+uint64_t append_Node_alloc(Node_alloc* list, char base)
+{
+   
+    if (list->length + 1 > list->size)
+    {
+        long long i = list->size;
+
+        ///list->topo_order这里用不到，所以不用先分配空间
+        ///但是还是一起分配了吧，免得麻烦
+        list->size = list->size * 2;
+        list->list = (Node*)realloc(list->list, sizeof(Node)*list->size);
+        ///list->topo_order = (uint64_t*)realloc(list->topo_order, sizeof(uint64_t)*list->size);
+        
+        for (; i < list->size; i++)
+        {
+            list->list[i].income_edges.list=NULL;
+            list->list[i].outcome_edges.list=NULL;
+            list->list[i].alignedTo_Nodes.list=NULL;
+        }
+    }
+    
+    list->list[list->length].ID = list->length;
+    list->list[list->length].base = base;
+    init_Edge_alloc(&list->list[list->length].income_edges);
+    init_Edge_alloc(&list->list[list->length].outcome_edges);
+    init_Edge_alloc(&list->list[list->length].alignedTo_Nodes);
+    
+    list->length++;
+
+    return list->length - 1;
+}
+
+
+
+
+
+
+
+
+
+
+
+void init_Graph(Graph* g)
+{
+    init_Node_alloc(&g->g_nodes);
+    g->g_n_edges = 0;
+    g->g_n_nodes = 0;
+    g->g_next_nodeID = 0;
+    g->s_end_nodeID = 0;
+    g->s_start_nodeID = 0;
+    g->seq = NULL;
+    g->seqID = (uint64_t)-1;
+}
+
+void destory_Graph(Graph* g)
+{
+    destory_Node_alloc(&g->g_nodes);
+}
+
+void clear_Graph(Graph* g)
+{
+    clear_Node_alloc(&g->g_nodes);
+
+    g->g_n_edges = 0;
+    g->g_n_nodes = 0;
+    g->g_next_nodeID = 0;
+    g->s_end_nodeID = 0;
+    g->s_start_nodeID = 0;
+    g->seq = NULL;
+    g->seqID = (uint64_t)-1;
+}
+
+
+
+
+
+uint64_t inline add_Node_Graph(Graph* g, char base)
+{
+    return append_Node_alloc(&g->g_nodes, base);
+}
+
+
+void inline add_Edge_Graph(Graph* g, uint64_t start, uint64_t end, uint64_t weight)
+{
+    if (start >= g->g_nodes.length || end >= g->g_nodes.length)
+    {
+        fprintf(stderr, "Not existing nodes ...");
+        exit(0);
+    }
+    
+    ///对起始节点加出边
+    append_Edge_alloc(&g->g_nodes.list[start].outcome_edges, start, end, weight);
+    ///对结束节点加入边
+    append_Edge_alloc(&g->g_nodes.list[end].income_edges, start, end, weight);
+}
+
+void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long* startID, long long* endID)
+{
+    long long firstID, lastID, nodeID, i;
+    firstID = -1;
+    lastID = -1;
+
+    if(g_read_length == 0)
+        return;
+    
+    for (i = 0; i < g_read_length; i++)
+    {
+        nodeID = add_Node_Graph(g, g_read_seq[i]);
+
+        ////fprintf(stderr, "nodeID: %llu\n", nodeID);
+        
+        if (firstID == -1)
+        {
+            firstID = nodeID;
+        }
+        if (lastID != -1)
+        {
+            add_Edge_Graph(g, lastID, nodeID, 1);
+        }
+
+        lastID = nodeID; 
+    }
+
+    *startID = firstID;
+    *endID = lastID;
+    
+}
+
+
+void Perform_POA(Graph* g, overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read)
+{
+    long long startNodeID, endNodeID;
+    ///第一条序列是read本身，g_read里存的是反向互补，所以首先要恢复回正向
+    ///这一步可以优化掉
+    reverse_complement(g_read->seq, g_read->length);
+    addUnmatchedSeqToGraph(g, g_read->seq, g_read->length, &startNodeID, &endNodeID);
+
+    /**
+    if (startNodeID!=0||endNodeID!=g_read->length-1)
+    {
+        fprintf(stderr, "Error startNodeID or endNodeID ...\n");
+    }
+    check_addUnmatchedSeqToGraph(g, g_read->seq, g_read->length, startNodeID, endNodeID);
+    **/
+
+   get_Topo_Sort_Order(&g->g_nodes, 0);
+
+   uint64_t i = 0;
+   for ( i = 0; i < overlap_list->length; i++)
+   {
+       /**
+       if(overlap_list->list[i].x_id == overlap_list->list[i].y_id)
+       {
+           fprintf(stderr, "Error x_id or y_id ...\n");
+       }
+       **/
+
+       if (overlap_list->list[i].y_pos_strand)
+       {
+           recover_UC_Read_RC(g_read, R_INF, overlap_list->list[i].y_id);
+       }
+       else
+       {
+           recover_UC_Read(g_read, R_INF, overlap_list->list[i].y_id);
+       }
+
+   }
+
+}
+
+void topologicalSortDFS(Node_alloc* list, uint64_t nodeID)
+{
+    list->sort.visit[nodeID] = 1;
+
+    long long i;
+    uint64_t out_nodeID;
+
+    for (i = 0; i < list->list[nodeID].outcome_edges.length; i++)
+    {
+        out_nodeID = list->list[nodeID].outcome_edges.list[i].out_node;
+        if (list->sort.visit[out_nodeID] == 0)
+        {
+            topologicalSortDFS(list, out_nodeID);
+        }
+    }
+
+    list->sort.length--;
+    list->sort.list[list->sort.length] = nodeID;
+}
+
+#define INIT_STACK(stack) stack.iterative_i = 0;
+#define PUSH(stack, nodeID, time) stack.iterative_buffer[stack.iterative_i]=nodeID;\
+stack.iterative_buffer_visit[stack.iterative_i++]=time;
+#define IF_EMPTY(stack) (stack.iterative_i == 0)
+#define POP(stack, nodeID, time) --stack.iterative_i;nodeID = stack.iterative_buffer[stack.iterative_i];\
+time = stack.iterative_buffer_visit[stack.iterative_i];
+
+
+void topologicalSortDFS_Iterative(Node_alloc* list, uint64_t nodeID)
+{
+    long long i;
+    uint64_t out_nodeID;
+    int flag;
+
+    INIT_STACK(list->sort);
+    PUSH(list->sort, nodeID, 0);
+
+    while (!IF_EMPTY(list->sort))
+    {
+        POP(list->sort, nodeID, flag);
+        ///flag == 1说明是第二次访问; flag == 0说明是第一次访问
+        if (flag)
+        {
+            list->sort.length--;
+            list->sort.list[list->sort.length] = nodeID;
+            continue;
+        }
+        
+        list->sort.visit[nodeID] = 1;
+        PUSH(list->sort, nodeID, 1);
+
+        for (i = 0; i < list->list[nodeID].outcome_edges.length; i++)
+        {
+            out_nodeID = list->list[nodeID].outcome_edges.list[i].out_node;
+            if (list->sort.visit[out_nodeID] == 0)
+            {
+                PUSH(list->sort, out_nodeID, 0);
+            }
+        }
+        
+    }
+}
+
+uint64_t* get_Topo_Sort_Order(Node_alloc* list, int need_sort)
+{
+    long long i = 0;
+    list->sort.length = list->length;
+    if (list->length > list->sort.size)
+    {
+        list->sort.size = list->length;
+        list->sort.list = (uint64_t*)realloc(list->sort.list, sizeof(uint64_t)*list->sort.size);
+        list->sort.visit = (uint8_t*)realloc(list->sort.visit, sizeof(uint8_t)*list->sort.size);
+
+        list->sort.iterative_buffer 
+            = (uint64_t*)realloc(list->sort.iterative_buffer, sizeof(uint64_t)*list->sort.size);
+        list->sort.iterative_buffer_visit 
+            = (uint8_t*)realloc(list->sort.iterative_buffer_visit, sizeof(uint8_t)*list->sort.size);
+    }
+    
+    if (!need_sort)
+    {
+        ///可以循环展开, 作用微乎其微
+        for (i = 0; i < list->length; i++)
+        {
+            list->sort.list[i] = i;
+        }
+               
+    }
+    else
+    {
+        memset(list->sort.visit, 0 , list->length);
+        for (i = 0; i < list->length; i++)
+        {
+            if(list->sort.visit[i] == 0)
+            {
+                ///topologicalSortDFS(list, i);
+                topologicalSortDFS_Iterative(list, i);
+            }
+        }
+
+
+        /**
+        for (i = 0; i < list->length; i++)
+        {
+            if (list->sort.list[i] != i)
+            {
+                fprintf(stderr, "ERROR Sort ....\n");
+            }
+        }
+        **/
+        
+
+    }
+    
+    return list->sort.list;
+    
+}