CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pfilter("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfilter);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (queryFileName == "not open") { abort = true; }
+ else { m->setFastaFile(queryFileName); }
referenceFileName = validParameter.validFile(parameters, "reference", true);
if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
namesFileName = validParameter.validFile(parameters, "name", true);
if(namesFileName == "not found"){ namesFileName = ""; }
else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
+ else { m->setNameFile(namesFileName); }
qualFileName = validParameter.validFile(parameters, "qfile", true);
if(qualFileName == "not found"){ qualFileName = ""; }
else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
-
+ else { m->setQualFile(qualFileName); }
+
reportFileName = validParameter.validFile(parameters, "report", true);
if(reportFileName == "not found"){ reportFileName = ""; }
else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
temp = validParameter.validFile(parameters, "ignorechimeras", false); if (temp == "not found") { temp = "T"; }
ignoreChimeras = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; }
- filter = m->isTrue(temp);
-
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
convert(temp, processors);
maxLength = 2000;
totalBases = 0;
totalMatches = 0;
-
- //run vertical filter on query and reference files.
- if (filter) {
- string inputString = "fasta=" + queryFileName + "-" + referenceFileName;
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
- m->mothurOut("Running command: filter.seqs(" + inputString + ") to improve processing time."); m->mothurOutEndLine();
-
- Command* filterCommand = new FilterSeqsCommand(inputString);
- filterCommand->execute();
-
- map<string, vector<string> > filenames = filterCommand->getOutputFiles();
-
- delete filterCommand;
-
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
-
- queryFileName = filenames["fasta"][0];
- referenceFileName = filenames["fasta"][1];
- }
string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
processIDS.clear();
map<char, vector<int> >::iterator it;
int num = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//loop through and create all the processes you want
while (process != processors) {
in.close(); remove(tempFile.c_str());
}
-
+#endif
return num;
}
catch(exception& e) {