//**********************************************************************************************************************
vector<string> SffInfoCommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- 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", "", "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);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ 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", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ 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); }
exit(1);
}
}
+
//**********************************************************************************************************************
-string SffInfoCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SffInfoCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "flow") { outputFileName = "flow"; }
- else if (type == "sfftxt") { outputFileName = "sff.txt"; }
- else if (type == "sff") { outputFileName = "sff"; }
- else if (type == "qfile") { outputFileName = "qual"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],fasta-[filename],[tag],fasta"; }
+ else if (type == "flow") { pattern = "[filename],flow"; }
+ else if (type == "sfftxt") { pattern = "[filename],sff.txt"; }
+ else if (type == "sff") { pattern = "[filename],[group],sff"; }
+ else if (type == "qfile") { pattern = "[filename],qual-[filename],[tag],qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
-
//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(){
try {
string rootName = outputDir + m->getRootName(m->getSimpleName(input));
if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
- string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("sfftxt");
- string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("flow");
- if (trim) {
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("qfile");
- }else{
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("qfile");
- }
-
+ map<string, string> variables;
+ variables["[filename]"] = rootName;
+ string sfftxtFileName = getOutputFileName("sfftxt",variables);
+ string outFlowFileName = getOutputFileName("flow",variables);
+ if (!trim) { variables["[tag]"] = "raw"; }
+ outFastaFileName = getOutputFileName("fasta",variables);
+ outQualFileName = getOutputFileName("qfile",variables);
+
if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
char buffer3 [4];
in.read(buffer3, 4);
header.indexLength = be_int4(*(unsigned int *)(&buffer3));
-
+
//read num reads
char buffer4 [4];
in.read(buffer4, 4);
in.read(mybuffer,8);
for (int i = 0; i < filehandlesHeaders.size(); i++) {
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ unsigned long long offset = 0;
+ char* thisbuffer = new char[8];
+ thisbuffer[0] = (offset >> 56) & 0xFF;
+ thisbuffer[1] = (offset >> 48) & 0xFF;
+ thisbuffer[2] = (offset >> 40) & 0xFF;
+ thisbuffer[3] = (offset >> 32) & 0xFF;
+ thisbuffer[4] = (offset >> 24) & 0xFF;
+ thisbuffer[5] = (offset >> 16) & 0xFF;
+ thisbuffer[6] = (offset >> 8) & 0xFF;
+ thisbuffer[7] = offset & 0xFF;
ofstream out;
m->openOutputFileAppend(filehandlesHeaders[i][j], out);
- out.write(mybuffer, in.gcount());
+ out.write(thisbuffer, 8);
out.close();
}
}
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
ofstream out;
m->openOutputFileAppend(filehandlesHeaders[i][j], out);
- out.write(mybuffer, in.gcount());
+ int offset = 0;
+ char* thisbuffer = new char[4];
+ thisbuffer[0] = (offset >> 24) & 0xFF;
+ thisbuffer[1] = (offset >> 16) & 0xFF;
+ thisbuffer[2] = (offset >> 8) & 0xFF;
+ thisbuffer[3] = offset & 0xFF;
+ out.write(thisbuffer, 4);
out.close();
}
}
for (int i = 0; i < filehandlesHeaders.size(); i++) {
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
ofstream out;
- m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
out.write(mybuffer, spot-spotInFile);
out.close();
}
char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
-
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
char * mybuffer;
mybuffer = new char [spot-startSpotInFile];
ifstream in2;
- m->openInputFile(currentFileName, in2);
+ in2.open(currentFileName.c_str(), ios::binary);
in2.seekg(startSpotInFile);
in2.read(mybuffer,spot-startSpotInFile);
in2.close();
if(trashCodeLength == 0){
ofstream out;
- m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
+ m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
out.write(mybuffer, in2.gcount());
out.close();
delete[] mybuffer;
}
else{
ofstream out;
- m->openOutputFileAppend(noMatchFile, out);
+ m->openOutputFileBinaryAppend(noMatchFile, out);
out.write(mybuffer, in2.gcount());
out.close();
delete[] mybuffer;
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- seq = "NNNN";
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
+ int endValue = header.clipQualRight;
//make the bases you want to clip lowercase and the bases you want to keep upper case
- if(header.clipQualRight == 0){ header.clipQualRight = seq.length(); }
+ if(endValue == 0){ endValue = seq.length(); }
for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
- for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}
for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
//make the bases you want to clip lowercase and the bases you want to keep upper case
- if(header.clipQualRight == 0){ header.clipQualRight = read.bases.length(); }
+ int endValue = header.clipQualRight;
+ if(endValue == 0){ endValue = read.bases.length(); }
for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { read.bases[i] = toupper(read.bases[i]); }
- for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { read.bases[i] = toupper(read.bases[i]); }
+ for (int i = (endValue-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- seq = "NNNN";
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
+ int endValue = header.clipQualRight;
//make the bases you want to clip lowercase and the bases you want to keep upper case
- if(header.clipQualRight == 0){ header.clipQualRight = seq.length(); }
+ if(endValue == 0){ endValue = seq.length(); }
for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
- for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- out << ">" << header.name << " xy=" << header.xy << endl;
- out << "0\t0\t0\t0";
+ if (header.clipQualRight == 0) { //don't trim right
+ out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }else {
+ out << ">" << header.name << " xy=" << header.xy << endl;
+ out << "0\t0\t0\t0";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
//**********************************************************************************************************************
int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
try {
- if(header.clipQualRight > header.clipQualLeft){
-
- int rightIndex = 0;
- for (int i = 0; i < header.clipQualRight; i++) { rightIndex += read.flowIndex[i]; }
-
- out << header.name << ' ' << rightIndex;
- for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
- out << endl;
- }
+
+ int endValue = header.clipQualRight;
+ if (header.clipQualRight == 0) {
+ endValue = read.flowIndex.size();
+ if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
+ }
+ if(endValue > header.clipQualLeft){
+
+ int rightIndex = 0;
+ for (int i = 0; i < endValue; i++) { rightIndex += read.flowIndex[i]; }
+
+ out << header.name << ' ' << rightIndex;
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
+ out << endl;
+ }
return 0;
fileRoot = m->getRootName(fileRoot);
}
- string outFlowFileName = outputDir + fileRoot + getOutputFileNameTag("flow");
- if (trim) {
- outFastaFileName = outputDir + fileRoot + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + fileRoot + getOutputFileNameTag("qfile");
- }else{
- outFastaFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("qfile");
- }
+ map<string, string> variables;
+ variables["[filename]"] = fileRoot;
+ string sfftxtFileName = getOutputFileName("sfftxt",variables);
+ string outFlowFileName = getOutputFileName("flow",variables);
+ if (!trim) { variables["[tag]"] = "raw"; }
+ outFastaFileName = getOutputFileName("fasta",variables);
+ outQualFileName = getOutputFileName("qfile",variables);
if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
// get rest of line in case there is a primer name
while (!inOligos.eof()) {
char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
}
ofstream temp;
- string thisFilename = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + comboGroupName + "." + getOutputFileNameTag("sff");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = comboGroupName;
+ string thisFilename = getOutputFileName("sff",variables);
if (uniqueNames.count(thisFilename) == 0) {
outputNames.push_back(thisFilename);
outputTypes["sff"].push_back(thisFilename);
numFPrimers = primers.size();
numLinkers = linker.size();
numSpacers = spacer.size();
- noMatchFile = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + "scrap." + getOutputFileNameTag("sff");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = "scrap";
+ noMatchFile = getOutputFileName("sff",variables);
m->mothurRemove(noMatchFile);
bool allBlank = true;
projects / mothur.git / blobdiff