//**********************************************************************************************************************
vector<string> SeqErrorCommand::getValidParameters(){
try {
- string Array[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
+ string Array[] = {"query", "reference", "name", "qfile", "report", "threshold", "ignorechimeras", "inputdir", "outputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ maxLength = 2000;
+
string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
m->openOutputFile(errorSummaryFileName, errorSummaryFile);
outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
m->openInputFile(qualFileName, qualFile);
report = ReportFile(reportFile, reportFileName);
- qualForwardMap.resize(1000);
- qualReverseMap.resize(1000);
- for(int i=0;i<1000;i++){
- qualForwardMap[i].assign(100,0);
- qualReverseMap[i].assign(100,0);
+ qualForwardMap.resize(maxLength);
+ qualReverseMap.resize(maxLength);
+ for(int i=0;i<maxLength;i++){
+ qualForwardMap[i].assign(maxLength,0);
+ qualReverseMap[i].assign(maxLength,0);
}
}
qScoreErrorMap['a'].assign(41, 0);
map<char, vector<int> > errorForward;
- errorForward['m'].assign(1000,0);
- errorForward['s'].assign(1000,0);
- errorForward['i'].assign(1000,0);
- errorForward['d'].assign(1000,0);
- errorForward['a'].assign(1000,0);
+ errorForward['m'].assign(maxLength,0);
+ errorForward['s'].assign(maxLength,0);
+ errorForward['i'].assign(maxLength,0);
+ errorForward['d'].assign(maxLength,0);
+ errorForward['a'].assign(maxLength,0);
map<char, vector<int> > errorReverse;
- errorReverse['m'].assign(1000,0);
- errorReverse['s'].assign(1000,0);
- errorReverse['i'].assign(1000,0);
- errorReverse['d'].assign(1000,0);
- errorReverse['a'].assign(1000,0);
+ errorReverse['m'].assign(maxLength,0);
+ errorReverse['s'].assign(maxLength,0);
+ errorReverse['i'].assign(maxLength,0);
+ errorReverse['d'].assign(maxLength,0);
+ errorReverse['a'].assign(maxLength,0);
string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
}
index++;
- if(index % 1000 == 0){ cout << index << endl; }
+
+ if(index % 1000 == 0){ m->mothurOut(toString(index) + '\n'); }
}
queryFile.close();
errorSummaryFile.close();
outputNames.push_back(errorForwardFileName); outputTypes["error.forward"].push_back(errorForwardFileName);
errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
- for(int i=0;i<1000;i++){
+ for(int i=0;i<maxLength;i++){
float match = (float)errorForward['m'][i];
float subst = (float)errorForward['s'][i];
float insert = (float)errorForward['i'][i];
outputNames.push_back(errorReverseFileName); outputTypes["error.reverse"].push_back(errorReverseFileName);
errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
- for(int i=0;i<1000;i++){
+ for(int i=0;i<maxLength;i++){
float match = (float)errorReverse['m'][i];
float subst = (float)errorReverse['s'][i];
float insert = (float)errorReverse['i'][i];