void GetSeqsCommand::readName(){
try {
- string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);;
+ string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
ofstream out;
openOutputFile(outputFileName, out);
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 1) {
validSecond.push_back(parsedNames[i]);
- names.erase(parsedNames[i]);
}
}
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
- names.erase(firstCol);
//make first name in set you come to first column and then add the remaining names to second column
}else {
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
void GetSeqsCommand::readAlign(){
try {
- string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile);;
+ string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
ofstream out;
openOutputFile(outputFileName, out);