【无标题】readCounter报错 BamStandardIndex ERROR: could not generate a summary of index file

文章指出在使用samtools创建的.index文件为bai格式,但readCounter软件要求的是.bam.bai格式。因此,为了解决这个问题,需要重新运行samtools以生成正确后缀的.index文件,即.bam.bai,确保软件能正确识别。

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明明是有用samtools建立的index,但是readCounter时却找不到

 

 报错原因,我在用samtools建立的index时生成的文件是bai,但是readCounter软件只认识.bam.bai后缀的index,不认识直接bai后缀的,所以这里index需要生成bam.bai。

解决方案:重新用samtools建立.bam.bai后缀的index即可

麻烦优化一下下列C++代码 void PIN_FAST_ANALYSIS_CALL onRead(THREADID threadid, ADDRINT memoryAddr){ ThreadData* t = get_tls(threadid); t->readCounter++; // get latest version value of this memory location map<ADDRINT, std::pair<vector<UINT32>, std::pair<THREADID, UINT32> > >::iterator it = t->shadowRead.find(memoryAddr); if (it != t->shadowRead.end()){ // if its in the thread's local memory /*(implementation of the last one value predictor)*/ // if it already exists. update the counter for the thread by 1 // for the location. it->second.first[threadid]++; } else { // if hasn't been read by current thread before //insert record into memoryMap vector <UINT32> temp(8,0); t->shadowRead[memoryAddr] = std::make_pair(temp, std::make_pair(0,0)); // insert pair of vector and another pair t->shadowRead[memoryAddr].first[threadid] = 1; } // Get last write to memoryAddr and save order with read in execution log PIN_GetLock(&writeLock, threadid + 1); rdOps++; unordered_map<ADDRINT, std::pair<vector<std::pair<THREADID, UINT32> > ,bool> >::iterator itt = memoryMap.find(memoryAddr); map<ADDRINT, std::pair<vector<UINT32>, std::pair<THREADID, UINT32> > >::iterator ita = t->shadowRead.find(memoryAddr); if ((itt != memoryMap.end()) && (itt->second.first.size() > 0) && (itt->second.first.back().first != t->tid) && (itt->second.first.back().first != ita->second.second.first && itt->second.first.back().second != ita->second.second.second)){ // optimize to weed out intra-thread dependencies on shared memory locations //EXECUTION LOG FORMAT WRITE-READ: WRITETHREAD WRITECOUNTER READ traceFileReads << itt->second.first.back().first << "," << itt->second.first.back().second << "," << t->tid << "," << t->readCounter << endl; } PIN_ReleaseLock(&writeLock);
07-25
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