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);
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";
//erase from file list
filenames.erase(filenames.begin()+i);
i--;
- }
+ }else { m->setSFFFile(filenames[i]); }
}
}
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"; }
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);
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 = "";
//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];
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{
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{
}
/* 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{