changed sffinfo flow default to true. fixed bug in trim.seqs and filter.seqs related...

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 207328203a24088c111054de2b157fae9235876c..e008ce47d2153530af1c0ab09a585a94d4963662 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -16,7 +16,7 @@ vector<string> SffInfoCommand::setParameters(){
                CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
                CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
                CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
-               CommandParameter pflow("flow", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflow);
+               CommandParameter pflow("flow", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pflow);
                CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
                CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
                CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
@@ -41,7 +41,7 @@ string SffInfoCommand::getHelpString(){
                helpString += "The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n";
                helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n";
                helpString += "The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n";
-               helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n";
+               helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=True. \n";
                helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n";
                helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
                helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
@@ -256,7 +256,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
                        fasta = m->isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
+                       temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "T";                             }
                        flow = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
@@ -303,7 +303,7 @@ int SffInfoCommand::execute(){
                
                for (int s = 0; s < filenames.size(); s++) {
                        
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
                        
                        int start = time(NULL);
                        
@@ -319,7 +319,7 @@ int SffInfoCommand::execute(){
                
                if (sfftxtFilename != "") {  parseSffTxt(); }
                
-               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
+               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
                
                //set fasta file as new current fastafile
                string current = "";
@@ -466,7 +466,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        //read offset
                        char buffer2 [8];
                        in.read(buffer2, 8);
-                       header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
+                       header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
                        
                        //read index length
                        char buffer3 [4];
@@ -513,8 +513,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        delete[] tempBuffer2;
                                
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
                        in.seekg(spot);
                        
                }else{
@@ -581,8 +581,8 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        decodeName(header.timestamp, header.region, header.xy, header.name);
                        
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{
@@ -634,8 +634,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
                        }
        
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{