changes while testing

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 704e752341320dd75b9f213658d74530583ec9cb..051c1dfb057c0148c3f0053f94707b7e6d034dc0 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -16,6 +16,7 @@ vector<string> ParseFastaQCommand::setParameters(){
                CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
                CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
                CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual);
+        CommandParameter ppacbio("pacbio", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppacbio);
                CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "sanger", "", "", "","",false,false,true); parameters.push_back(pformat);
         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -39,6 +40,7 @@ string ParseFastaQCommand::getHelpString(){
                helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=sanger.\n";
         helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
         helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
+        helpString += "The pacbio parameter allows you to indicate .... When set to true, quality scores of 0 will results in a corresponding base of N. Default=F.\n";
                helpString += "Example fastq.info(fastaq=test.fastaq).\n";
                helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
                return helpString;
@@ -132,7 +134,11 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        fasta = m->isTrue(temp); 
 
                        temp = validParameter.validFile(parameters, "qfile", false);    if(temp == "not found"){        temp = "T";     }
-                       qual = m->isTrue(temp); 
+                       qual = m->isTrue(temp);
+            
+            temp = validParameter.validFile(parameters, "pacbio", false);      if(temp == "not found"){        temp = "F";     }
+                       pacbio = m->isTrue(temp);
+
                        
             format = validParameter.validFile(parameters, "format", false);            if (format == "not found"){     format = "sanger";      }
             
@@ -185,7 +191,7 @@ int ParseFastaQCommand::execute(){
                        else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        else { 
                 name = name.substr(1); 
-                for (int i = 0; i < name.length(); i++) { if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; } }
+                m->checkName(name);
             }
                        
                        //read sequence
@@ -198,7 +204,7 @@ int ParseFastaQCommand::execute(){
                        else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        else { 
                 name2 = name2.substr(1);  
-                for (int i = 0; i < name2.length(); i++) { if (name2[i] == ':') { name2[i] = '_'; m->changedSeqNames = true; } }
+                m->checkName(name2);
             }
                        
                        //read quality scores
@@ -209,22 +215,33 @@ int ParseFastaQCommand::execute(){
                        if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
                        if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
-                       //print sequence info to files
-                       if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
-                       
-                       if (qual) { 
-                               vector<int> qualScores = convertQual(quality);
+            vector<int> qualScores;
+            if (qual) {
+                               qualScores = convertQual(quality);
                                outQual << ">" << name << endl;
                                for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
                                outQual << endl;
                        }
+            
+            if (m->control_pressed) { break; }
+            
+            if (pacbio) {
+                if (!qual) { qualScores = convertQual(quality); } //get scores if we didn't already
+                for (int i = 0; i < qualScores.size(); i++) {
+                    if (qualScores[i] == 0){ sequence[i] = 'N'; }
+                }
+            }
+            
+                       //print sequence info to files
+                       if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
+                       
                }
                
                in.close();
                if (fasta)      { outFasta.close();     }
                if (qual)       { outQual.close();      }
                
-               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); outputNames.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
                
                //set fasta file as new current fastafile
                string current = "";