if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
- appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+ m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
- appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+ m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
m->mothurRemove(nonBlankAccnosFiles[h]);
}
}else { //recreate the accnosfile if needed
else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
for (int i = 1; i < processors; i++) {
- appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
+ m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
m->mothurRemove((alignFileName + toString(i) + ".temp"));
appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
- appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+ m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
m->mothurRemove(nonBlankAccnosFiles[h]);
}
}else { //recreate the accnosfile if needed
exit(1);
}
}
-/**************************************************************************************************/
-
-void AlignCommand::appendAlignFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream input;
- m->openOutputFileAppend(filename, output);
- m->openInputFile(temp, input);
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "appendAlignFiles");
- exit(1);
- }
-}
//**********************************************************************************************************************
void AlignCommand::appendReportFiles(string temp, string filename) {
while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
+ char buffer[4096];
+ while (!input.eof()) {
+ input.read(buffer, 4096);
+ output.write(buffer, input.gcount());
+ }
input.close();
output.close();
int driver(linePair*, string, string, string, string);
int createProcesses(string, string, string, string);
- void appendAlignFiles(string, string);
void appendReportFiles(string, string);
#ifdef USE_MPI
else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
for(int i=0;i<processIDS.size();i++){
- appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
- appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+ m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
+ m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
}else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp")); }
rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
- appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+ m->appendFiles(nonBlankAccnosFiles[h], accnos);
m->mothurRemove(nonBlankAccnosFiles[h]);
}
}else { //recreate the accnosfile if needed
exit(1);
}
}
-/**************************************************************************************************/
-
-void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream input;
- m->openOutputFileAppend(filename, output);
- m->openInputFile(temp, input);
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
- exit(1);
- }
-}
-
//**********************************************************************************************************************
int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
bool abort, probs, save, flip;
int driver(linePair*, string, string, string, string);
- void appendTaxFiles(string, string);
int createProcesses(string, string, string, string);
string addUnclassifieds(string, int);
int ConsensusSeqsCommand::readNames(){
try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
+ map<string, string> temp;
+ map<string, string>::iterator it;
+ bool error = false;
+
+ m->readNames(namefile, temp); //use central buffered read
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+ string thisname, repnames;
+ thisname = itTemp->first;
+ repnames = itTemp->second;
+
+ it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
-
+ nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
}else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
+ }
+
if (error) { m->control_pressed = true; }
return 0;
//names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
map<string, string> repNames;
- int numUniqueNamesFile = readNames(repNames);
+ int numUniqueNamesFile = m->readNames(repnamesfile, repNames);
//are there the same number of otus in the fasta and name files
if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
exit(1);
}
}
-/**********************************************************************************************************************/
-int CreateDatabaseCommand::readNames(map<string, string>& nameMap) {
- try {
-
- //open input file
- ifstream in;
- m->openInputFile(repnamesfile, in);
-
- while (!in.eof()) {
- if (m->control_pressed) { break; }
-
- string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
-
- nameMap[secondCol] = firstCol;
- }
- in.close();
-
- return nameMap.size();
-
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "readNames");
- exit(1);
- }
-}
//**********************************************************************************************************************
ListVector* CreateDatabaseCommand::getList(){
try {
vector<int> readFasta(vector<Sequence>&);
vector<int> readTax(vector<string>&);
- int readNames(map<string, string>&);
ListVector* getList();
};
/************************************************************/
int GroupMap::readMap() {
- string seqName, seqGroup;
+ try {
+ string seqName, seqGroup;
int error = 0;
-
- while(fileHandle){
- fileHandle >> seqName; m->gobble(fileHandle); //read from first column
- fileHandle >> seqGroup; //read from second column
-
- if (m->control_pressed) { fileHandle.close(); return 1; }
-
- setNamesOfGroups(seqGroup);
-
- it = groupmap.find(seqName);
-
- if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
- else {
- groupmap[seqName] = seqGroup; //store data in map
- seqsPerGroup[seqGroup]++; //increment number of seqs in that group
- }
- m->gobble(fileHandle);
- }
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ setNamesOfGroups(seqGroup);
+
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
fileHandle.close();
+
m->setAllGroups(namesOfGroups);
return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readMap");
+ exit(1);
+ }
}
/************************************************************/
int GroupMap::readDesignMap() {
- string seqName, seqGroup;
+ try {
+ string seqName, seqGroup;
int error = 0;
-
- while(fileHandle){
- fileHandle >> seqName; m->gobble(fileHandle); //read from first column
- fileHandle >> seqGroup; //read from second column
-
- if (m->control_pressed) { fileHandle.close(); return 1; }
-
- setNamesOfGroups(seqGroup);
-
- it = groupmap.find(seqName);
-
- if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine(); }
- else {
- groupmap[seqName] = seqGroup; //store data in map
- seqsPerGroup[seqGroup]++; //increment number of seqs in that group
- }
- m->gobble(fileHandle);
- }
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ setNamesOfGroups(seqGroup);
+
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
fileHandle.close();
+
m->setAllGroups(namesOfGroups);
return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readDesignMap");
+ exit(1);
+ }
}
/************************************************************/
int GroupMap::readDesignMap(string filename) {
- groupFileName = filename;
- m->openInputFile(filename, fileHandle);
- index = 0;
- string seqName, seqGroup;
- int error = 0;
-
- while(fileHandle){
- fileHandle >> seqName; m->gobble(fileHandle); //read from first column
- fileHandle >> seqGroup; //read from second column
-
- if (m->control_pressed) { fileHandle.close(); return 1; }
-
- setNamesOfGroups(seqGroup);
-
- it = groupmap.find(seqName);
+ try {
+ groupFileName = filename;
+ m->openInputFile(filename, fileHandle);
+ index = 0;
+ string seqName, seqGroup;
+ int error = 0;
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
- if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine(); }
- else {
- groupmap[seqName] = seqGroup; //store data in map
- seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ setNamesOfGroups(seqGroup);
+
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
}
- m->gobble(fileHandle);
+ fileHandle.close();
+
+ m->setAllGroups(namesOfGroups);
+ return error;
}
- fileHandle.close();
- m->setAllGroups(namesOfGroups);
- return error;
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readDesignMap");
+ exit(1);
+ }
}
/************************************************************/
int GroupMap::getNumGroups() { return namesOfGroups.size(); }
int numLines = 0;
if (ableToOpen == 0) { //you opened it
- while(!input.eof()){
- char c = input.get();
- if(input.eof()) { break; }
- else { output << c; if (c == '\n') {numLines++;} }
- }
+
+ char buffer[4096];
+ while (!input.eof()) {
+ input.read(buffer, 4096);
+ output.write(buffer, input.gcount());
+ //count number of lines
+ for (int i = 0; i < input.gcount(); i++) { if (buffer[i] == '\n') {numLines++;} }
+ }
input.close();
}
exit(1);
}
}
+/***********************************************************************/
+
+vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
+ try {
+ vector<string> pieces;
+
+ for (int i = 0; i < size; i++) {
+ if (!isspace(buffer[i])) { rest += buffer[i]; }
+ else {
+ pieces.push_back(rest); rest = "";
+ while (i < size) { //gobble white space
+ if (isspace(buffer[i])) { i++; }
+ else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "parsePieces");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
try {
//open input file
ifstream in;
openInputFile(namefile, in);
-
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
-
- nameMap[firstCol] = secondCol;
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
+ }
}
in.close();
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
-
- vector<string> temp;
- splitAtComma(secondCol, temp);
-
- nameMap[firstCol] = temp;
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+ nameMap[firstCol] = temp;
+ pairDone = false;
+ }
+ }
}
in.close();
-
+
return nameMap.size();
-
}
catch(exception& e) {
errorOut(e, "MothurOut", "readNames");
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol; gobble(in);
- in >> secondCol; gobble(in);
-
- int num = getNumNames(secondCol);
-
- nameMap[firstCol] = num;
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
}
- in.close();
+ in.close();
return nameMap;
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
-
- int num = getNumNames(secondCol);
-
- map<string, string>::iterator it = fastamap.find(firstCol);
- if (it == fastamap.end()) {
- error = 1;
- mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
- }else {
- seqPriorityNode temp(num, it->second, firstCol);
- nameVector.push_back(temp);
- }
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ int num = getNumNames(secondCol);
+
+ map<string, string>::iterator it = fastamap.find(firstCol);
+ if (it == fastamap.end()) {
+ error = 1;
+ mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(num, it->second, firstCol);
+ nameVector.push_back(temp);
+ }
+
+ pairDone = false;
+ }
+ }
}
- in.close();
-
+ in.close();
+
return error;
-
}
catch(exception& e) {
errorOut(e, "MothurOut", "readNames");
string getline(istringstream&);
void gobble(istream&);
void gobble(istringstream&);
+ vector<string> splitWhiteSpace(string& rest, char[], int);
map<string, int> readNames(string);
int readNames(string, map<string, string>&);
int readNames(string, map<string, vector<string> >&);
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
- int readNames();
int getSummary(vector<unsigned long long>&);
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
int SubSampleCommand::readNames() {
try {
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, vector<string> >::iterator it;
-
- while(!in.eof()){
-
- if (m->control_pressed) { in.close(); return 0; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
- if (it == nameMap.end()) {
-
- vector<string> splitRepNames;
- m->splitAtComma(repnames, splitRepNames);
-
- nameMap[thisname] = splitRepNames;
- for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
-
- }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
-
- m->gobble(in);
- }
- in.close();
-
+ nameMap.clear();
+ m->readNames(namefile, nameMap);
+
+ //save names of all sequences
+ map<string, vector<string> >::iterator it;
+ for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
+
return 0;
}
currQual.printQScores(trimQualFile);
}
+
if(nameFile != ""){
map<string, string>::iterator itName = nameMap.find(currSeq.getName());
if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+ int numRedundants = 0;
if (nameFile != "") {
map<string, string>::iterator itName = nameMap.find(currSeq.getName());
if (itName != nameMap.end()) {
vector<string> thisSeqsNames;
m->splitAtChar(itName->second, thisSeqsNames, ',');
+ numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
}
}
map<string, int>::iterator it = groupCounts.find(thisGroup);
- if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
- else { groupCounts[it->first]++; }
+ if (it == groupCounts.end()) { groupCounts[thisGroup] = 1 + numRedundants; }
+ else { groupCounts[it->first] += (1 + numRedundants); }
}
}
outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+ int numRedundants = 0;
if (pDataArray->nameFile != "") {
map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
if (itName != pDataArray->nameMap.end()) {
vector<string> thisSeqsNames;
pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
+ numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
}
}
map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
- if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1; }
- else { pDataArray->groupCounts[it->first]++; }
+ if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
+ else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
}
}
projects / mothur.git / commitdiff