string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
//flow.files = 9 character offset
- compositeFASTAFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+ compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
m->openOutputFile(compositeFASTAFileName, temp);
temp.close();
- compositeNamesFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+ compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
m->openOutputFile(compositeNamesFileName, temp);
temp.close();
}
if(compositeNamesFileName != ""){
- m->appendFiles(nameFileName, uchimecompositeNamesFileName);
+ m->appendFiles(nameFileName, compositeNamesFileName);
}
}
catch(exception& e) {
}
uniqueFlowDataIntI.resize(numFlowCells * numUniques);
uniqueLengths.resize(numUniques);
- uniqueFlowgrams.resize(numFlowCells * numUniques);
-
+
flowDataPrI.resize(numSeqs * numFlowCells, 0);
for(int i=0;i<flowDataPrI.size();i++) { if (m->control_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]); }