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improve speed

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This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
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4
POA.cpp
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@@ -283,7 +283,7 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
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)
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
add_insertionEdge_weight(backbone, currentNodeID, y_string + y_i, operationLen);
backbone->g_nodes.list[currentNodeID].num_insertions++;
@@ -295,7 +295,7 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
///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)
///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