added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d8ebe50fb11859367256a28286dec9789cc70d36..0dc15f59ee98d0ee2d93659c4c3ad1f033f8a193 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -298,7 +298,7 @@ int SeqErrorCommand::execute(){
                if(qualFileName == "")  {       qLines = lines; rLines = lines; } //fills with duds
                
                int numSeqs = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                if(processors == 1){
                        numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
                }else{
@@ -366,7 +366,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                processIDS.clear();
                map<char, vector<int> >::iterator it;
                int num = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                
                //loop through and create all the processes you want
                while (process != processors) {
@@ -682,7 +682,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        if(numParentSeqs > 1 && ignoreChimeras == 1)    {       ignoreSeq = 1;  }
                        else                                                                                    {       ignoreSeq = 0;  }
                        
-                       Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
+                       Compare minCompare;
+            getErrors(query, referenceSeqs[closestRefIndex], minCompare);
                        
                        if(namesFileName != ""){
                                it = weights.find(query.getName());
@@ -739,7 +740,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        
                        index++;
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                unsigned long long pos = queryFile.tellg();
                                if ((pos == -1) || (pos >= line.end)) { break; }
                        #else
@@ -839,7 +840,7 @@ void SeqErrorCommand::getReferences(){
 
 //***************************************************************************************************************
 
-Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
+int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){
        try {
                if(query.getAlignLength() != reference.getAlignLength()){
                        m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
@@ -850,7 +851,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                string r = reference.getAligned();
 
                int started = 0;
-               Compare errors;
+               //Compare errors;
 
                for(int i=0;i<alignLength;i++){
 //                     cout << r[i] << '\t' << q[i] << '\t';
@@ -929,7 +930,8 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                errors.queryName = query.getName();
                errors.refName = reference.getName();
                
-               return errors;
+               //return errors;
+        return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "SeqErrorCommand", "getErrors");
@@ -1215,7 +1217,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 
 int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                //set file positions for fasta file
                fastaFilePos = m->divideFile(filename, processors);