sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 93e18e82f374c9fa5bad6a90f6fc2ff56e20246a..b17d9ed6799d9c8287664cf63241b0fde01bf40e 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,14 +14,14 @@
 //**********************************************************************************************************************
 vector<string> FilterSeqsCommand::setParameters(){     
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
-               CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
-               CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
-               CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+               CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+               CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+               CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+               CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -57,6 +57,22 @@ string FilterSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string FilterSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],filter.fasta"; } 
+        else if (type == "filter") {  pattern =  "[filename],filter"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -125,7 +141,12 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        fasta = validParameter.validFile(parameters, "fasta", false);
                        if (fasta == "not found") {                             
                                fasta = m->getFastaFile(); 
-                               if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               if (fasta != "") { 
+                    fastafileNames.push_back(fasta);  
+                    m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+                    string simpleName = m->getSimpleName(fasta);
+                    filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else { 
@@ -272,9 +293,10 @@ int FilterSeqsCommand::execute() {
                ofstream outFilter;
                
                //prevent giantic file name
-               string filterFile;
-               if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
-               else {  filterFile = outputDir + filterFileName + ".filter";  }
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + filterFileName + ".";
+               if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+               string filterFile = getOutputFileName("filter", variables);  
                
                m->openOutputFile(filterFile, outFilter);
                outFilter << filter << endl;
@@ -337,7 +359,9 @@ int FilterSeqsCommand::filterSequences() {
                        
                                for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                
-                               string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+                               string filteredFasta = getOutputFileName("fasta", variables);
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;
@@ -705,6 +729,9 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, strin
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
@@ -1152,6 +1179,9 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             F.mergeFilter(pDataArray[i]->F.getFilter());
             
                        for (int k = 0; k < alignmentLength; k++) {      F.a[k] += pDataArray[i]->F.a[k];       }