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注释了一些调试代码

This commit is contained in:
zzh 2025-04-14 13:56:45 +08:00
parent ee45166765
commit 32920ffe64
3 changed files with 27 additions and 19 deletions
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4
src/markdup/markdup.cpp
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@ -153,6 +153,10 @@ int MarkDuplicates() {
spdlog::info("{} duplicate reads found", dupIdxQue.Size()); spdlog::info("{} duplicate reads found", dupIdxQue.Size());
spdlog::info("{} optical reads found", opticalIdxQue.Size()); spdlog::info("{} optical reads found", opticalIdxQue.Size());
// spdlog::info("{} represent reads found", repIdxQue.Size()); // spdlog::info("{} represent reads found", repIdxQue.Size());
// dupIdxQue.RealSize("na12878.dup");
// opticalIdxQue.RealSize("normal.odup");
// return 0;
uint64_t bamIdx = 0; uint64_t bamIdx = 0;
DupInfo dupIdx = dupIdxQue.Pop(); DupInfo dupIdx = dupIdxQue.Pop();

18
src/markdup/md_types.h
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@ -272,16 +272,22 @@ struct DupIdxQueue {
return len - popNum; return len - popNum;
} }
uint64_t RealSize() { uint64_t RealSize(const string fileName) {
if (this->Size() == 0) {
return 0;
}
uint64_t len = 0; uint64_t len = 0;
auto preTop = minHeap.top(); auto preTop = minHeap.top();
DupInfo dupIdx = this->Pop(); DupInfo dupIdx = this->Pop();
DupInfo nextDup = dupIdx; DupInfo nextDup = dupIdx;
auto topIdx = minHeap.top(); auto topIdx = minHeap.top();
// ofstream ofs("n.dup"); ofstream ofs1("n-all.dup"); ofstream ofs(fileName); // ofstream ofs1(filePrefix + ".odup");
while (dupIdx != -1) { while (dupIdx != -1) {
ofs << dupIdx.idx << endl; // ofs1 << topIdx.arrId << '\t' << topIdx.arrIdx << '\t' << topIdx.dupIdx << endl;
++len; ++len;
while (true) { while (true) {
topIdx = minHeap.top(); topIdx = minHeap.top();
@ -295,14 +301,12 @@ struct DupIdxQueue {
<< endl; << endl;
} }
} }
// ofs << topIdx.dupIdx << endl; ofs1 << topIdx.arrId << '\t' << topIdx.arrIdx << '\t' << topIdx.dupIdx << endl;
dupIdx = nextDup; dupIdx = nextDup;
preTop = topIdx; preTop = topIdx;
} }
// ofs.close(); ofs1.close(); ofs.close(); // ofs1.close();
// cout << "RealSize: " << len << endl; cout << "RealSize: " << len << endl;
return len; return len;
} }
}; };

24
src/markdup/read_ends.h
View File

@ -147,12 +147,12 @@ struct ReadEnds : PhysicalLocation {
comp = a.read2ReferenceIndex - b.read2ReferenceIndex; comp = a.read2ReferenceIndex - b.read2ReferenceIndex;
if (comp == 0) if (comp == 0)
comp = a.read2Coordinate - b.read2Coordinate; comp = a.read2Coordinate - b.read2Coordinate;
if (comp == 0) // if (comp == 0)
comp = a.tile - b.tile; // comp = a.tile - b.tile;
if (comp == 0) // if (comp == 0)
comp = a.x - b.x; // 由于picard的bug，用short类型来表示x，y，导致其可能为负数 // comp = a.x - b.x; // 由于picard的bug，用short类型来表示x，y，导致其可能为负数
if (comp == 0) // if (comp == 0)
comp - a.y - b.y; // comp - a.y - b.y;
if (comp == 0) if (comp == 0)
comp = (int)(a.read1IndexInFile - b.read1IndexInFile); comp = (int)(a.read1IndexInFile - b.read1IndexInFile);
if (comp == 0) if (comp == 0)
@ -170,12 +170,12 @@ struct ReadEnds : PhysicalLocation {
comp = a.read2Coordinate - b.read2Coordinate; comp = a.read2Coordinate - b.read2Coordinate;
if (comp == 0) // 这个放在坐标比较了之后，把坐标范围的放在之前，这样对分段数据块比较好处理 if (comp == 0) // 这个放在坐标比较了之后，把坐标范围的放在之前，这样对分段数据块比较好处理
comp = a.orientation - b.orientation; comp = a.orientation - b.orientation;
if (comp == 0) // if (comp == 0)
comp = a.tile - b.tile; // comp = a.tile - b.tile;
if (comp == 0) // if (comp == 0)
comp = a.x - b.x; // 由于picard的bug，用short类型来表示x，y，导致其可能为负数 // comp = a.x - b.x; // 由于picard的bug，用short类型来表示x，y，导致其可能为负数
if (comp == 0) // if (comp == 0)
comp - a.y - b.y; // comp - a.y - b.y;
if (comp == 0) if (comp == 0)
comp = (int)(a.read1IndexInFile - b.read1IndexInFile); comp = (int)(a.read1IndexInFile - b.read1IndexInFile);
if (comp == 0) if (comp == 0)