added flag to count table read so that commands that don't require the group info...

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 7798a4d74f749eed04d4554c796776a58697b98b..be167d9b9cbb92a8ffea832b8c2eccfb4ed6bf3d 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -249,7 +249,7 @@ int BinSeqCommand::execute(){
                
                //if user gave a namesfile then use it
                if (namesfile != "") {  readNamesFile();  }
-        if (countfile != "") {  ct.readTable(countfile);  }
+        if (countfile != "") {  ct.readTable(countfile, true);  }
                
                input = new InputData(listfile, "list");
                list = input->getListVector();

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index fd94fcab7e289590da462eef7f03fc7069ab551f..cea481bd22062b7461a06705d08ba4d1c1930451 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -516,7 +516,7 @@ int ChimeraPerseusCommand::execute(){
             
             if (hasCount) {
                 CountTable* ct = new CountTable();
-                ct->readTable(nameFile);
+                ct->readTable(nameFile, true);
                 
                 if (ct->hasGroupInfo()) {
                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
@@ -534,7 +534,7 @@ int ChimeraPerseusCommand::execute(){
                     
                     if(processors == 1)        {       numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
                         if (dups) {
-                            CountTable c; c.readTable(nameFile);
+                            CountTable c; c.readTable(nameFile, true);
                             if (!m->isBlank(newCountFile)) {
                                 ifstream in2;
                                 m->openInputFile(newCountFile, in2);
@@ -559,7 +559,7 @@ int ChimeraPerseusCommand::execute(){
                         numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
                     }else {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        CountTable c; c.readTable(newCountFile, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1070,7 +1070,7 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
                int num = 0;
                
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(name); }
+        if (hasCount && dups) { newCount.readTable(name, true); }
         
                //sanity check
                if (groups.size() < processors) { processors = groups.size(); }

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 99a66f8838e4ccbbe10fe72ef66135be7dfda869..b6d4fc9323f659abe52cd70a1e3598a84d9db936 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -130,7 +130,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile);
+            ct->readTable(pDataArray->namefile, true);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index e7003c4d88bfe40266dffcf0770e3037cb39f38f..f01bd3ee9d9bb3611b52b38819f98300da9cff39 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -759,7 +759,7 @@ int ChimeraSlayerCommand::execute(){
                                if (processors == 1) {
                     numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile);
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFileNames[s]);
+                        CountTable c; c.readTable(nameFileNames[s], true);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -791,7 +791,7 @@ int ChimeraSlayerCommand::execute(){
                     }else {
                         if (hasCount) {
                             set<string> doNotRemove;
-                            CountTable c; c.readTable(newCountFile);
+                            CountTable c; c.readTable(newCountFile, true);
                             vector<string> namesInTable = c.getNamesOfSeqs();
                             for (int i = 0; i < namesInTable.size(); i++) {
                                 int temp = c.getNumSeqs(namesInTable[i]);
@@ -1551,7 +1551,7 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(countFile); }
+        if (hasCount && dups) { newCount.readTable(countFile, true); }
                
                int groupsPerProcessor = fileToPriority.size() / processors;
                int remainder = fileToPriority.size() % processors;
@@ -2161,7 +2161,7 @@ map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string na
         int error;
         if (hasCount) { 
             CountTable ct;
-            ct.readTable(nameFile);
+            ct.readTable(nameFile, true);
             
             for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                 int num = ct.getNumSeqs(it->first);

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 3d23a7693818f329ff6ac53cca560998c8a9fc95..422792a68525b495008694360c393e26ba358c09 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -674,7 +674,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile);
+                    ct.readTable(nameFile, true);
                     for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                         int num = ct.getNumSeqs(it->first);
                         if (num == 0) { error = 1; }
@@ -725,7 +725,7 @@ int ChimeraUchimeCommand::execute(){
                                if(processors == 1)     {       totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
                     
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFile);
+                        CountTable c; c.readTable(nameFile, true);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -755,7 +755,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        CountTable c; c.readTable(newCountFile, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1795,7 +1795,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
                int num = 0;
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(nameFile); }
+        if (hasCount && dups) { newCount.readTable(nameFile, true); }
                
                //sanity check
                if (groups.size() < processors) { processors = groups.size(); }

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 2237493801aa836dcb84e77e3957a480f30dcc2b..fadc4a4d401dcf5da93d0d32c56ed9ec8a7ef99a 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -175,7 +175,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile);
+            ct->readTable(pDataArray->namefile, true);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d0ddc691236e59cdd0fcb6a2578249375fd8ad0e..170c234ac245e6c32e3174ad80145fbcc359f2f2 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::execute(){
                if (namefile != "")     {       m->readNames(namefile, nameMap, true);  }
         if (groupfile != "")    {   groupMap = new GroupMap(groupfile);  groupMap->readMap();  groups = groupMap->getNamesOfGroups(); }
         else { groupMap = NULL;  }
-        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
         else {  ct = NULL;    }
         
                //read taxonomy file and save in map for easy access in building bin trees

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index edbd4c466bfa500bcaa72b1f8266f3dd40185ae9..b311821b3e8d293daac13107eb9e6771be360bf0 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -812,7 +812,7 @@ int ClassifySeqsCommand::execute(){
                 PhyloSummary* taxaSum;
                 if (hasCount) { 
                     ct = new CountTable();
-                    ct->readTable(countfileNames[s]);
+                    ct->readTable(countfileNames[s], true);
                     taxaSum = new PhyloSummary(taxonomyFileName, ct);
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {

diff --git a/clustercommand.cpp b/clustercommand.cpp
index e4e20622cae08b3578e8e8871616c1cd874da0aa..2ac2eaa6bd2466df296e407e7e67f9c8a095edc3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -305,7 +305,7 @@ int ClusterCommand::execute(){
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             read->read(ct);
         }else { read->read(nameMap); }
                

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 91eb923ae38d8b9a52ebb8a00a4ea4fb0cf951a7..08a5938b85b3b40f7a53619766d1a9a3e004a9a5 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -226,7 +226,7 @@ int ClusterDoturCommand::execute(){
             delete nameMap;
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             cluster->readPhylipFile(phylipfile, ct);
             delete ct;
         }else {

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 1b8cc71706710a3c80d53f6ff2fd877d07d98103..f17c11e7384330c4b9eb4d5af86f734fc0d0f21f 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -181,7 +181,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
             countfile = validParameter.validFile(parameters, "count", true);
                        if (countfile == "not open") { abort = true; countfile = ""; }  
                        else if (countfile == "not found") { countfile = ""; }
-                       else { ct.readTable(countfile); m->setCountTableFile(countfile); }
+                       else { ct.readTable(countfile, false); m->setCountTableFile(countfile); }
                        
             if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
                        

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 37e42d2fb167591825a26e6599c6986ee78e4f78..74867ebdeb0ec271d07d727b7cf9c8d19aa13284 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -1168,7 +1168,7 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
             cluster->readPhylipFile(thisDistFile, nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             cluster->readPhylipFile(thisDistFile, ct);
         }
         tag = cluster->getTag();
@@ -1296,7 +1296,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             read->read(ct);
         }else { read->read(nameMap); }
                

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 1b1e7d20d37603610945f6dadbf6dd32399ed8d5..3d671f98420e0fa7cf844aac647bd43feea959e8 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -226,7 +226,7 @@ int ConsensusSeqsCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                if (namefile != "") { readNames(); }
-        if (countfile != "") { ct.readTable(countfile);  }
+        if (countfile != "") { ct.readTable(countfile, true);  }
                
                if (m->control_pressed) { return 0; }
                

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 6da077485c5fcd7641d759ceb6820dc9652033a7..83c2d315d0b8f781caa02c04c4fed5e1cb6b6a0d 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -261,7 +261,7 @@ int CountGroupsCommand::execute(){
             m->openOutputFile(outputFileName, out);
             
                        CountTable ct;
-                       ct.readTable(countfile);
+                       ct.readTable(countfile, true);
             
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index dfa012eeff0f0f49c778c00b2098348a489f1855..e97810effcb6f3c2dd05a34f30518aea8f13a97b 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -17,6 +17,7 @@ vector<string> CountSeqsCommand::setParameters(){
        try {
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
                CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
+        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -39,6 +40,7 @@ string CountSeqsCommand::getHelpString(){
                helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
                helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
+        helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
                helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
                helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
                helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";

diff --git a/countseqscommand.h b/countseqscommand.h
index b4170a8867897b96e13f7483f6053b960f7629b4..6ba36b1a0264e20efe7bd251bc8d505cdf30cb87 100644 (file)
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -37,6 +37,7 @@ private:
        string namefile, groupfile, outputDir, groups;
        bool abort, large;
        vector<string> Groups, outputNames;
+    int processors;
     
     int processSmall(string);
     int processLarge(string);

diff --git a/counttable.cpp b/counttable.cpp
index 48b52d98e76e6da585c862682c3906bdf4ad0f67..6eca8ee2a4b5354da54412b9eb6986b6ba244657 100644 (file)
--- a/counttable.cpp
+++ b/counttable.cpp
@@ -211,7 +211,7 @@ int CountTable::createTable(string namefile, string groupfile, bool createGroup)
        }
 }
 /************************************************************/
-int CountTable::readTable(string file) {
+int CountTable::readTable(string file, bool readGroups) {
     try {
         filename = file;
         ifstream in;
@@ -227,7 +227,7 @@ int CountTable::readTable(string file) {
         indexNameMap.clear();
         counts.clear();
         map<int, string> originalGroupIndexes;
-        if (columnHeaders.size() > 2) { hasGroups = true; numGroups = columnHeaders.size() - 2;  }
+        if ((columnHeaders.size() > 2) && readGroups) { hasGroups = true; numGroups = columnHeaders.size() - 2;  }
         for (int i = 2; i < columnHeaders.size(); i++) {  groups.push_back(columnHeaders[i]);  originalGroupIndexes[i-2] = columnHeaders[i]; totalGroups.push_back(0); }
         //sort groups to keep consistent with how we store the groups in groupmap
         sort(groups.begin(), groups.end());
@@ -248,7 +248,13 @@ int CountTable::readTable(string file) {
             
             //if group info, then read it
             vector<int> groupCounts; groupCounts.resize(numGroups, 0);
-            for (int i = 0; i < numGroups; i++) {  int thisIndex = indexGroupMap[originalGroupIndexes[i]]; in >> groupCounts[thisIndex]; m->gobble(in); totalGroups[thisIndex] += groupCounts[thisIndex];  }
+            if (columnHeaders.size() > 2) { //file contains groups
+                if (readGroups) { //user wants to save them
+                    for (int i = 0; i < numGroups; i++) {  int thisIndex = indexGroupMap[originalGroupIndexes[i]]; in >> groupCounts[thisIndex]; m->gobble(in); totalGroups[thisIndex] += groupCounts[thisIndex];  }
+                }else { //read and discard
+                    m->getline(in); m->gobble(in);
+                }
+            }
             
             map<string, int>::iterator it = indexNameMap.find(name);
             if (it == indexNameMap.end()) {

diff --git a/counttable.h b/counttable.h
index 34c941bece659b832afd9f2ff8866a16d37c14f1..51d0b4544bc73c7e832826bad702028f0143a549 100644 (file)
--- a/counttable.h
+++ b/counttable.h
@@ -50,7 +50,7 @@ class CountTable {
         //reads and creates smart enough to eliminate groups with zero counts 
         int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames 
         int createTable(string, string, bool); //namefile, groupfile, createGroup
-        int readTable(string); 
+        int readTable(string, bool);
     
         int printTable(string);
         int printHeaders(ofstream&);

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 09e077b57ca8800d3663f6dd5c3515102aaa1129..8b73425fc5c2aefb2d7e3b4a87caf4fa8be44c40 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
         }
         CountTable ct;
         if (countfile != "")  {  
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             if (countfile == outCountFile){
                 //prepare filenames and open files
                 map<string, string> mvariables;

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e4f7450b4291e1ca281ebe806dd476fac86019b9..45e0a783e393ba828d8bd74c3884fa45779a92f2 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -370,7 +370,7 @@ int GetGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
                 
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 438aa3808441e60b9fb4fa22d4e9313a58956b2a..b895cc4fc62bfb49346c96df7a0d6371dd2b4a50 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -444,7 +444,7 @@ int GetLineageCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
 

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index a041b38aadac3c3cc28bf7313eeb4e8bde6e4535..dbd19a8bfc7d5a266b131e74b18f3f2980c40aba 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -261,7 +261,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 if (ct.hasGroupInfo()) { hasGroups = true; }
             }
             
@@ -1106,7 +1106,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile);
+            thisCt.readTable(countfile, true);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
     
@@ -1253,7 +1253,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile);
+            thisCt.readTable(countfile, true);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
         

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 4870a627663da88857f157e0cfd2912545a7aa61..da1bfae2c07f5cb719961dce93324ff8135fbfc4 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -319,7 +319,7 @@ int GetRAbundCommand::execute(){
 int GetRAbundCommand::processList(ofstream& out){
        try {
         CountTable ct;
-        ct.readTable(countfile);
+        ct.readTable(countfile, false);
         
         InputData input(inputfile, format);
         ListVector* list = input.getListVector();

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index d3fb5298c5d1191c0f90b4787b6b2ed349de5f61..f4838cf8a72a75708085b3917b8828939e43f683 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -307,7 +307,7 @@ int GetSAbundCommand::execute(){
 int GetSAbundCommand::processList(ofstream& out){
        try {
         CountTable ct;
-        ct.readTable(countfile);
+        ct.readTable(countfile, false);
         
         InputData input(inputfile, format);
         ListVector* list = input.getListVector();

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 287f5a6acdc08a9c40b6e2e12b159a2f83fc9636..142023e7a40881c1c6397a761ba350132490b75c 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -587,7 +587,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
                

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 98739b68291fd42d83d1190a46313886126f02bf..01a60aea3b01ad2ce95584c33280e7dde4d8147f 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -543,7 +543,7 @@ int HeatMapSimCommand::runCommandDist() {
                 }
              }else if (countfile != "") {
                 nameMap = NULL;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 names = ct.getNamesOfSeqs();
             }
                        

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d10dfb4935c390d0353976eeb5c182340519ebfb..cf884705cb26f341ef08713b118af32fd49c5bdf 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -415,7 +415,7 @@ int ListSeqsCommand::readGroup(){
 int ListSeqsCommand::readCount(){
        try {
                CountTable ct;
-               ct.readTable(countfile);
+               ct.readTable(countfile, false);
         
         if (m->control_pressed) { return 0; }
         

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 24c4f27777d21ed88b6f3b41411394502802404e..e76dd4860b03826db116323af7e42528a591c526 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -247,7 +247,7 @@ int MGClusterCommand::execute(){
         if(countfile != "") {
             //map<string, int> nameMapCounts = m->readNames(namefile);
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             rabund = new RAbundVector();
             createRabund(ct, list, rabund);
         }else {

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 3ed65c67f700b98d3c99a12a9dc6018ff4cfdd76..5a568f3511d38f56601362d860a9643e702c9a1b 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -169,7 +169,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 if (!ct.hasGroupInfo()) { 
                     abort = true;
                     m->mothurOut("[ERROR]: The parse.list command requires group info to be present in your countfile, quitting."); m->mothurOutEndLine();

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 8db6c24ff05ce4a5a23bc11a9021b208f5e65d55..f2ca9db29d7a94ce0d22606d4ad114e11001fd4f 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -1088,7 +1088,7 @@ int PcrSeqsCommand::readCount(set<string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }
                

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index bbf8df27ac5ee691f091f150638b781f85486a11..24d22845c5a4fc33d109888e5f2007d25134672e 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }

diff --git a/primerdesigncommand.cpp b/primerdesigncommand.cpp
index 59369b3cf7411bdc0383d2a0be0676c3caee4c61..195adf4f716b29bd7c12a2f3529603e4baec6b4d 100644 (file)
--- a/primerdesigncommand.cpp
+++ b/primerdesigncommand.cpp
@@ -1088,7 +1088,7 @@ map<string, int> PrimerDesignCommand::readCount(unsigned long int& numSeqs){
         map<string, int> nameMap;
         
         CountTable ct;
-        ct.readTable(countfile);
+        ct.readTable(countfile, false);
         vector<string> namesOfSeqs = ct.getNamesOfSeqs();
         numSeqs = ct.getNumUniqueSeqs();
         

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 4f4b1580582b953c3b8318acc68345cc8d45ae48..1e5fe11de39f34b30f59249895bcf393506e32f9 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -369,7 +369,7 @@ int RemoveGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
             
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 5b6fc252c4ae8c78619d0f3ad76afbb9792cbddd..1496f8a69b74896f610889bbf87771f9237d89da 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -599,7 +599,7 @@ int RemoveLineageCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
                

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index cf6674e5a7cbfd65c9e17e4a22cd24678502239f..a551681fb6721e4b3670fe912e1b6bfe909dd388 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -411,7 +411,7 @@ int RemoveRareCommand::processList(){
                        util.setGroups(Groups, namesGroups);
                        m->openOutputFile(outputGroupFileName, outGroup);
                }else if (countfile != "") {
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             if (ct.hasGroupInfo()) {
                 vector<string> namesGroups = ct.getNamesOfGroups();
                 SharedUtil util;

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index c7af108325390221bd0313e4ad2a733dfd2e90d3..b1bc4fd508576c04126206b4e178798c088cb91d 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -557,7 +557,7 @@ int RemoveSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
 

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index d2fbe935356a2f0752efa683a893a5892e1b2eb2..051aa99434f6bb21a8d3b3b54cb2cc671eab98d2 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -683,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -714,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -1019,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
                        if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
                        getSummary(positions); 
@@ -2206,7 +2206,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }
                

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c1cdb6b90c910c2e58c5d016a6c2293f7d7aa8ce..3354665852ce1b5a95b9ecc7cc673d5083b25d8b 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -200,7 +200,7 @@ int AlignCheckCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
                

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 203a71ede5544a3d1c5e2eba73072fa825445aac..54d3dcc5c9b6c93f267478e6491126b3aedff772 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
                if(namesFileName != "")     {   weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             weights = ct.getNameMap();
         }
                

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 6d8336cb40217a9547791e69765230dff0dabe62..27bb8d95190fb66ea03510cf266d2d53824d988c 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -203,7 +203,7 @@ int SeqSummaryCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
                

diff --git a/sequencecountparser.cpp b/sequencecountparser.cpp
index 1300c0f1023fdd24d53c7bb9033be1d5c1c3e5d6..37eb4e7f5256617bd3917428616a897ee14706e4 100644 (file)
--- a/sequencecountparser.cpp
+++ b/sequencecountparser.cpp
@@ -16,7 +16,7 @@ SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
                
                //read count file
                CountTable countTable;
-               countTable.readTable(countfile);
+               countTable.readTable(countfile, true);
                
                //initialize maps
                namesOfGroups = countTable.getNamesOfGroups();

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 91ca1a15cc7b3d6bad67331e129b57c6819e34b4..8d5d89c3a96843b5fd1c8aafa112f25c3b216e1f 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -766,7 +766,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
             m->setAllGroups(allGroups);
         }else{
             countTable = new CountTable();
-            countTable->readTable(countfile);
+            countTable->readTable(countfile, true);
         }
         
         if (m->control_pressed) { return 0; }

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 223ca073fa2c5c9c083d5d20bc024fe82f724b68..0ee2f795cea302bd98a31285b278479f13ef17f3 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -32,7 +32,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
             groupmap->readMap(); 
         }else {
             countTable = new CountTable();
-            countTable->readTable(m->getCountTableFile());
+            countTable->readTable(m->getCountTableFile(), true);
         }
 
                int hold;

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 2d37e8d459857f7f0161ba87111df0403ff9c827..580493b60a1e4d449a71b8689635e8ced4dea397 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -212,7 +212,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
             }
             
             if ((namefile != "") && (countfile != "")) {

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 238eda55e04a3df6e43a2fae8cee5736c4f6febc..c15ba3a4d588b3eedcaca7713c6d5acb8610aee2 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -320,7 +320,7 @@ int SplitGroupCommand::runCount(){
        try {
         
         CountTable ct;
-        ct.readTable(countfile);
+        ct.readTable(countfile, true);
         if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, cannot split by group.\n"); m->control_pressed = true; }
         
         if (m->control_pressed) { return 0; }

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 4128191598d22e8e7280f403dca79494e61da948..fe79fbbae883a409187730e1899fde8b05493193 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -273,7 +273,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
             }
             
             if ((namefile != "") && (countfile != "")) {

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 0f6f719ef568446af70438eb08579a81c7c6f3f6..e1e626ea273a650840dd849442e43762e9a100cf 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -196,7 +196,7 @@ int SummaryQualCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
                else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
         

diff --git a/summarytaxcommand.cpp b/summarytaxcommand.cpp
index c76f175b047ef9ee46eff28911c1a21cd6310a97..e244863c65de54c6c5133d3901a1dc1bc973c6ac 100644 (file)
--- a/summarytaxcommand.cpp
+++ b/summarytaxcommand.cpp
@@ -223,7 +223,7 @@ int SummaryTaxCommand::execute(){
             groupMap->readMap();
         }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, true);
         }
                
         PhyloSummary* taxaSum;

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index b793dc885ef9213f290f118be55066a0e2837086..0119741988c010e0d3b3d3df1bbc4c052f5bba8f 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -458,7 +458,7 @@ int TreeGroupCommand::execute(){
                 readMatrix->read(nameMap);
             }else if (countfile != "") {
                 ct = new CountTable();
-                ct->readTable(countfile);
+                ct->readTable(countfile, true);
                 readMatrix->read(ct);
             }else {
                 readMatrix->read(nameMap);

diff --git a/treereader.cpp b/treereader.cpp
index 0e25f12a39b2a5341ad2ba3bf7255bb8b6aa7edc..8427b562501086e8a9bf13b6e036474348412b0e 100644 (file)
--- a/treereader.cpp
+++ b/treereader.cpp
@@ -15,7 +15,7 @@ TreeReader::TreeReader(string tf, string cf) : treefile(tf), countfile(cf)  {
     try {
         m = MothurOut::getInstance();
         ct = new CountTable();
-        ct->readTable(cf);
+        ct->readTable(cf, true);
         
         //if no groupinfo in count file we need to add it
         if (!ct->hasGroupInfo()) {

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5a5d445cb8624386e90d4c714c1f460f1be0d509..81b9111b17dd8bba332ad8a8267cc12bf16e235a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
                
                if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             nameCount = ct.getNameMap();
                        outputNames.push_back(trimCountFile);
                        outputNames.push_back(scrapCountFile);
@@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile);
+                ct->readTable(trimCountFile, true);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;