vector<string> parsedNames;
//parse second column saving each name
while (secondCol.find_first_of(',') != -1) {
name = secondCol.substr(0,secondCol.find_first_of(','));
secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
parsedNames.push_back(name);
vector<string> parsedNames;
//parse second column saving each name
while (secondCol.find_first_of(',') != -1) {
name = secondCol.substr(0,secondCol.find_first_of(','));
secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
parsedNames.push_back(name);
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 0) {
validSecond.push_back(parsedNames[i]);
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 0) {
validSecond.push_back(parsedNames[i]);
//if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) == 0) {
//if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) == 0) {
//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 RemoveSeqsCommand::readAlign(){
try {
//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 RemoveSeqsCommand::readAlign(){
try {