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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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POA.cpp
+9 -583
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@@ -191,7 +191,7 @@ void init_Node_alloc(Node_alloc* list)
list->sort.iterative_buffer_visit = NULL;
long long i;
uint64_t i;
for (i = 0; i < list->size; i++)
{
list->list[i].insertion_edges.list=NULL;
@@ -238,10 +238,8 @@ uint64_t append_Node_alloc(Node_alloc* list, char base)
if (list->length + 1 > list->size)
{
long long i = list->size;
uint64_t 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);
@@ -336,8 +334,6 @@ void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length,
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)
{
@@ -345,12 +341,7 @@ void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length,
}
if (lastID != -1)
{
/**
///0是match边
add_Edge_Graph(g, lastID, nodeID, 0);
**/
///只有match边长度是0
///mismatch边长度都是1
///the legnth of match edge is 0, while the length of musmatch is 1
append_Edge_alloc(&(g->g_nodes.list[lastID].mismatch_edges), lastID, nodeID, 1, 0);
}
@@ -367,287 +358,6 @@ void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length,
inline void add_insertionEdge_weight_print(Graph* g, long long alignNodeID, char* insert, long long insert_length)
{
long long nodeID;
long long edgeID;
Edge_alloc* edge = &(g->g_nodes.list[alignNodeID].insertion_edges);
/******************************for homopolymer*************************/
long long i = 0;
char hom;
if (insert_length > 0)
{
hom = insert[0];
}
for (i = 0; i < insert_length; i++)
{
if(insert[i] != hom)
{
break;
}
}
fprintf(stderr, "###insert_length: %d\n", insert_length);
///if it is a homopolymer
if(i == insert_length)
{
///single base
edgeID = getEdge(g, edge, 1, insert[0]);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else ///不存在这么一条边
{
nodeID = add_Node_Graph(g, insert[0]);
append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
///将新加入的节点通过insertion_edges接回backbone上
///应该连回到原节点，而不是原节点的下一个节点
///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
}
///multiple bases
for (i = 1; i < insert_length; i++)
{
edgeID = get_insertion_Edges(g, edge, i + 1, insert);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else
{
create_insertion_Edges(g, alignNodeID, i + 1, insert);
}
}
return;
}
/******************************for homopolymer*************************/
fprintf(stderr, "###not homopolymer: %d\n", insert_length);
if (insert_length == 1)
{
edgeID = getEdge(g, edge, 1, insert[0]);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else ///不存在这么一条边
{
nodeID = add_Node_Graph(g, insert[0]);
append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
///将新加入的节点通过insertion_edges接回backbone上
///应该连回到原节点，而不是原节点的下一个节点
///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
}
}
else if (insert_length == 2)
{
/*******************第0个字符********************* */
edgeID = getEdge(g, edge, 1, insert[0]);
fprintf(stderr, "edgeID[0]: %d, length: %d\n", edgeID, edge->list[edgeID].length);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else ///不存在这么一条边
{
nodeID = add_Node_Graph(g, insert[0]);
append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
///将新加入的节点通过insertion_edges接回backbone上
///应该连回到原节点，而不是原节点的下一个节点
///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
}
fprintf(stderr, "edge->length: %d\n", edge->length);
/*******************第0个字符********************* */
/*******************第1个字符********************* */
if (insert[1] != insert[0])
{
edgeID = getEdge(g, edge, 1, insert[1]);
fprintf(stderr, "edgeID[1]: %d, length: %d\n", edgeID, edge->list[edgeID].length);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else ///不存在这么一条边
{
nodeID = add_Node_Graph(g, insert[1]);
append_Edge_alloc(edge, alignNodeID, nodeID, 1, 1);
///将新加入的节点通过insertion_edges接回backbone上
///应该连回到原节点，而不是原节点的下一个节点
///append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID + 1, 1, 0);
append_Edge_alloc(&(g->g_nodes.list[nodeID].insertion_edges), nodeID, alignNodeID, 1, 0);
}
fprintf(stderr, "edge->length: %d\n", edge->length);
}
/*******************第1个字符********************* */
/**********************两个字符******************* */
edgeID = get_insertion_Edges(g, edge, 2, insert);
fprintf(stderr, "edgeID[len2]: %d, length: %d\n", edgeID, edge->list[edgeID].length);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else
{
create_insertion_Edges(g, alignNodeID, insert_length, insert);
}
fprintf(stderr, "edge->length: %d\n", edge->length);
for (i = 0; i < edge->length; i++)
{
fprintf(stderr, "edgeID[%d].length: %d\n", i, edge->list[i].length);
}
/**********************两个字符******************* */
}
else if (insert_length > 2)
{
////fprintf(stderr, "too long insertion\n");
/*************************大于2个字符************************** */
edgeID = get_insertion_Edges(g, edge, insert_length, insert);
if (edgeID != -1)
{
///这条路均只有一个出度
edge->list[edgeID].weight++;
}
else
{
create_insertion_Edges(g, alignNodeID, insert_length, insert);
}
}
}
void addmatchedSeqToGraph_print(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end)
{
int x_i, y_i, cigar_i;
x_i = 0;
y_i = 0;
cigar_i = 0;
int operation;
int operationLen;
int i;
int last_operation = -1;
fprintf(stderr,"*******\n");
///note that node 0 is the start node
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2是x缺字符（y多字符），而3是y缺字符（x多字符）
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
// fprintf(stderr, "operation: %d, operationLen: %d\n",
// operation, operationLen);
///这种情况代表匹配和mismatch
if (operation == 0 || operation == 1)
{
for (i = 0; i < operationLen; i++)
{
//backbone->g_nodes.list[currentNodeID].weight++;
///前面是插入，后面有可能是误配，也有可能是匹配
add_mismatchEdge_weight(backbone, currentNodeID, y_string[y_i], last_operation);
x_i++;
y_i++;
currentNodeID++;
}
}///insertion
else if (operation == 2)
{
///cigar的起始和结尾不可能是2，所以这里-1没问题
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
add_insertionEdge_weight_print(backbone, currentNodeID, y_string + y_i, operationLen);
backbone->g_nodes.list[currentNodeID].num_insertions++;
}
///fprintf(stderr, "y_string: %.*s\n", operationLen, y_string+y_i);
y_i += operationLen;
}
else if (operation == 3)
{
///3是y缺字符（x多字符），也就是backbone多字符
///这个相当于在backbone对应字符处变成了‘——’
///因此可以用mismatch类似的方法处理
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
///add_deletion_to_backbone(backbone, &currentNodeID, operationLen);
///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
///为了保险要不还给他加上吧
///先不加
add_deletionEdge_weight(backbone, currentNodeID, operationLen);
}
currentNodeID += operationLen;
x_i += operationLen;
}
last_operation = operation;
cigar_i++;
}
/**
///cigar的起始和结尾不可能是2
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);
}
**/
}
void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end)
{
@@ -664,20 +374,19 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
///note that node 0 is the start node
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2是x缺字符（y多字符），而3是y缺字符（x多字符）
///2 mean y has more bases, while 3 means x has more bases
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
///这种情况代表匹配和mismatch
///match/mismatch
if (operation == 0 || operation == 1)
{
for (i = 0; i < operationLen; i++)
{
//backbone->g_nodes.list[currentNodeID].weight++;
///前面是插入，后面有可能是误配，也有可能是匹配
///if the previous node is insertion, this node might be mismatch/match
add_mismatchEdge_weight(backbone, currentNodeID, y_string[y_i], last_operation);
x_i++;
y_i++;
@@ -686,7 +395,7 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
}///insertion
else if (operation == 2)
{
///cigar的起始和结尾不可能是2，所以这里-1没问题
///the begin and end of cigar cannot be 2, so -1 is right here
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
add_insertionEdge_weight(backbone, currentNodeID, y_string + y_i, operationLen);
@@ -696,15 +405,10 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
}
else if (operation == 3)
{
///3是y缺字符（x多字符），也就是backbone多字符
///这个相当于在backbone对应字符处变成了‘——’
///因此可以用mismatch类似的方法处理
///3 means x has more bases, that means backbone has more bases
///like a mismatch (-)
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
///add_deletion_to_backbone(backbone, &currentNodeID, operationLen);
///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
///为了保险要不还给他加上吧
///先不加
add_deletionEdge_weight(backbone, currentNodeID, operationLen);
}
@@ -720,284 +424,6 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
}
void debug_graph(Graph* g, long long backbone_length)
{
long long i = 0;
if (g->s_start_nodeID != 0 || g->s_end_nodeID != backbone_length)
{
fprintf(stderr, "error\n");
}
for (i = g->s_start_nodeID; i <= g->s_end_nodeID; i++)
{
if(g->g_nodes.list[i].weight != 1)
{
fprintf(stderr, "error node weight\n");
}
if(g->g_nodes.list[i].mismatch_edges.length > 4)
{
fprintf(stderr, "error mismatch_edges\n");
}
if(g->g_nodes.list[i].mismatch_edges.length < 1 && i != g->s_end_nodeID)
{
fprintf(stderr, "i: %d, error mismatch_edges: %d\n", i, g->g_nodes.list[i].mismatch_edges.length);
}
}
for (i = 0; i < g->g_nodes.length; i++)
{
if(g->g_nodes.list[i].ID < g->s_start_nodeID || g->g_nodes.list[i].ID > g->s_end_nodeID)
{
if (g->g_nodes.list[i].deletion_edges.length +
g->g_nodes.list[i].insertion_edges.length +
g->g_nodes.list[i].mismatch_edges.length
!= 1)
{
fprintf(stderr, "g->s_start_nodeID: %lld\n",
g->s_start_nodeID);
fprintf(stderr, "g->s_end_nodeID: %lld\n",
g->s_end_nodeID);
fprintf(stderr, "deletion_edges_length: %lld\n",
g->g_nodes.list[i].deletion_edges.length);
fprintf(stderr, "insertion_edges_length: %lld, \n",
g->g_nodes.list[i].insertion_edges.length);
fprintf(stderr, "g->g_nodes.list[i].insertion_edges.list[0].length: %lld, \n",
g->g_nodes.list[i].insertion_edges.list[0].length);
fprintf(stderr, "g->g_nodes.list[i].insertion_edges.list[1].length: %lld, \n",
g->g_nodes.list[i].insertion_edges.list[1].length);
fprintf(stderr, "mismatch_edges_length: %lld\n",
g->g_nodes.list[i].mismatch_edges.length);
}
else
{
///不是0肯定是1
if (g->g_nodes.list[i].deletion_edges.length != 0)
{
long long step = g->g_nodes.list[i].deletion_edges.list[0].length;
long long nodeID = i;
for (int j = 0; j < step; j++)
{
nodeID = g->g_nodes.list[nodeID].deletion_edges.list[0].out_node;
}
nodeID = g->g_nodes.list[nodeID].deletion_edges.list[0].out_node;
if (nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID)
{
fprintf(stderr, "error\n");
}
}
if (g->g_nodes.list[i].insertion_edges.length != 0)
{
long long step = g->g_nodes.list[i].insertion_edges.list[0].length;
long long nodeID = i;
for (int j = 0; j < step; j++)
{
nodeID = g->g_nodes.list[nodeID].insertion_edges.list[0].out_node;
}
nodeID = g->g_nodes.list[nodeID].insertion_edges.list[0].out_node;
if ((nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID))
{
fprintf(stderr, "error: step: %d\n", step);
}
}
if (g->g_nodes.list[i].mismatch_edges.length != 0)
{
long long step = g->g_nodes.list[i].mismatch_edges.list[0].length;
long long nodeID = i;
for (int j = 0; j < step; j++)
{
nodeID = g->g_nodes.list[nodeID].mismatch_edges.list[0].out_node;
}
nodeID = g->g_nodes.list[nodeID].mismatch_edges.list[0].out_node;
if (nodeID < g->s_start_nodeID || nodeID > g->s_end_nodeID)
{
fprintf(stderr, "error\n");
}
}
}
}
}
}
void Graph_debug(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end)
{
/**
int x_i, y_i, cigar_i;
x_i = 0;
y_i = 0;
cigar_i = 0;
int operation;
int operationLen;
int i;
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2是x缺字符（y多字符），而3是y缺字符（x多字符）
///while (x_i < x_len && y_i < y_len && cigar_i < cigar->length)
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
///这种情况代表匹配
if (operation == 0)
{
for (i = 0; i < operationLen; i++)
{
if (backbone->g_nodes.list[currentNodeID].base != y_string[y_i])
{
fprintf(stderr, "error match\n");
}
backbone->g_nodes.list[currentNodeID].weight--;
x_i++;
y_i++;
currentNodeID++;
}
}
else if (operation == 1)
{
for (i = 0; i < operationLen; i++)
{
if (backbone->g_nodes.list[currentNodeID].base == y_string[y_i])
{
fprintf(stderr, "error mismatch 1\n");
}
long long mismatchID = get_alignToNode(backbone, currentNodeID, y_string[y_i]);
if(mismatchID == -1)
{
fprintf(stderr, "error mismatch 2\n");
}
else
{
backbone->g_nodes.list[mismatchID].weight--;
}
x_i++;
y_i++;
currentNodeID++;
}
}
else if (operation == 2)
{
long long nodeID = currentNodeID - 1;
long long mismatchID;
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);
}
**/
}