if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ int start = time(NULL);
+
m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += hasPath(filenames[s]); }
string outputFileName = outputDir + getRootName(getSimpleName(filenames[s])) + "sff.txt";
- extractSffInfo(filenames[s], outputFileName);
+ int numReads = extractSffInfo(filenames[s], outputFileName);
outputNames.push_back(outputFileName);
- m->mothurOut("Done."); m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//**********************************************************************************************************************
int SffInfoCommand::extractSffInfo(string input, string output){
try {
+
ofstream out;
openOutputFile(output, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
ifstream in;
in.open(input.c_str(), ios::binary);
- CommonHeader* header = new CommonHeader();
+ CommonHeader header;
readCommonHeader(in, header);
- cout << strlen(header->flowChars) << endl;
- //cout << "magic = " << header->magicNumber << endl << "version = " << header->version << endl << "index offset = " << header->indexOffset << endl << "index length = "<< header->indexLength << endl << "numreads = " << header->numReads << endl << "header length = " << header->headerLength << endl << "key length = " << header->keyLength << endl;
-//cout << "numflowreads = "<< header->numFlowsPerRead << endl << "flow format code = "<< header->flogramFormatCode << endl << "flow chars = " << header->flowChars << endl << "key sequence = " << header->keySequence << endl << endl;
- cout << in.tellg() << endl;
+ int count = 0;
+
+ //check magic number and version
+ if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
+ if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
+
//read through the sff file
while (!in.eof()) {
//print common header
- printCommonHeader(out, header, true);
+ printCommonHeader(out, header);
//read header
- Header* readheader = new Header();
+ Header readheader;
readHeader(in, readheader);
-
- cout << in.tellg() << endl;
-
+
//print header
- printHeader(out, readheader, true);
+ printHeader(out, readheader);
//read data
- seqRead* read = new seqRead();
- readSeqData(in, read, header->numFlowsPerRead, readheader->numBases);
+ seqRead read;
+ readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
+
+ //print data
+ printSeqData(out, read);
- cout << in.tellg() << endl;
+ count++;
- //print data
- printSeqData(out, read, true);
+ //report progress
+ if((count+1) % 500 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
+
+ if (m->control_pressed) { count = 0; break; }
- delete readheader;
- delete read;
+ if (count >= header.numReads) { break; }
}
+ //report progress
+ if (!m->control_pressed) { if((count) % 500 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
+
in.close();
out.close();
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "extractSffInfo");
}
}
//**********************************************************************************************************************
-int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader* header){
+int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
try {
if (!in.eof()) {
//read magic number
- char buffer[sizeof(header->magicNumber)];
- in.read(buffer, sizeof(header->magicNumber));
- header->magicNumber = be_int4(*(unsigned int *)(&buffer));
- //delete[] buffer;
- cout << "here " << header->magicNumber << '\t' << in.tellg() << endl;
+ char buffer[sizeof(header.magicNumber)];
+ in.read(buffer, sizeof(header.magicNumber));
+ header.magicNumber = be_int4(*(unsigned int *)(&buffer));
+
//read version
- header->version = new char(4);
- in.read(header->version, 4);
- string tempBuf0 = header->version; //this is in here because the read sometimes tacks on extra chars, not sure why?
- if (tempBuf0.length() > 4) { tempBuf0 = tempBuf0.substr(0, 4); strcpy(header->version, tempBuf0.c_str()); }
- //memcpy(header->version, buffer+4, 4);
- cout << "here " << header->version << '\t' << in.tellg() << endl;
+ char buffer9[4];
+ in.read(buffer9, 4);
+ header.version = "";
+ for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
+
//read offset
- char buffer2 [sizeof(header->indexOffset)];
- in.read(buffer2, sizeof(header->indexOffset));
- header->indexOffset = be_int8(*(unsigned long int *)(&buffer2));
- //delete[] buffer;
- cout << "here " << header->indexOffset << '\t' << in.tellg() << endl;
+ char buffer2 [sizeof(header.indexOffset)];
+ in.read(buffer2, sizeof(header.indexOffset));
+ header.indexOffset = be_int8(*(unsigned long int *)(&buffer2));
+
//read index length
- char buffer3 [sizeof(header->indexLength)];
- in.read(buffer3, sizeof(header->indexLength));
- header->indexLength = be_int4(*(unsigned int *)(&buffer3));
- //delete[] buffer;
- cout << "here " << header->indexLength << '\t' << in.tellg() << endl;
+ char buffer3 [sizeof(header.indexLength)];
+ in.read(buffer3, sizeof(header.indexLength));
+ header.indexLength = be_int4(*(unsigned int *)(&buffer3));
+
//read num reads
- char buffer4 [sizeof(header->numReads)];
- in.read(buffer4, sizeof(header->numReads));
- header->numReads = be_int4(*(unsigned int *)(&buffer4));
- //delete[] buffer;
- cout << "here " << header->numReads << '\t' << in.tellg() << endl;
+ char buffer4 [sizeof(header.numReads)];
+ in.read(buffer4, sizeof(header.numReads));
+ header.numReads = be_int4(*(unsigned int *)(&buffer4));
+
//read header length
- char buffer5 [sizeof(header->headerLength)];
- in.read(buffer5, sizeof(header->headerLength));
- header->headerLength = be_int2(*(unsigned short *)(&buffer5));
- //delete[] buffer;
- cout << "here " << header->headerLength << '\t' << in.tellg() << endl;
+ char buffer5 [sizeof(header.headerLength)];
+ in.read(buffer5, sizeof(header.headerLength));
+ header.headerLength = be_int2(*(unsigned short *)(&buffer5));
+
//read key length
- char buffer6 [sizeof(header->keyLength)];
- in.read(buffer6, sizeof(header->keyLength));
- header->keyLength = be_int2(*(unsigned short *)(&buffer6));
- //delete[] buffer;
-
-cout << "here " << header->keyLength << '\t' << in.tellg() << endl;
+ char buffer6 [sizeof(header.keyLength)];
+ in.read(buffer6, sizeof(header.keyLength));
+ header.keyLength = be_int2(*(unsigned short *)(&buffer6));
+
//read number of flow reads
- char buffer7 [sizeof(header->numFlowsPerRead)];
- in.read(buffer7, sizeof(header->numFlowsPerRead));
- header->numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
- //delete[] buffer;
- cout << "here " << header->numFlowsPerRead << '\t' << in.tellg() << endl;
+ char buffer7 [sizeof(header.numFlowsPerRead)];
+ in.read(buffer7, sizeof(header.numFlowsPerRead));
+ header.numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
+
//read format code
- //buffer = new char(sizeof(header->flogramFormatCode));
- in.read(&header->flogramFormatCode, 1);
- header->flogramFormatCode = be_int1(*(char *)(&header->flogramFormatCode));
- //delete[] buffer;
- cout << "here " << header->flogramFormatCode << '\t' << in.tellg() << endl;
-
+ char buffer8 [1];
+ in.read(buffer8, 1);
+ header.flogramFormatCode = (int)(buffer8[0]);
+
//read flow chars
- //header->numFlowsPerRead = 800;
- header->flowChars = new char(header->numFlowsPerRead);
- //buffer = new char(header->numFlowsPerRead);
- cout << "here" << endl;
- in.read(header->flowChars, header->numFlowsPerRead);
- //string tempBuf1 = header->flowChars + '\0'; //this is in here because the read sometimes tacks on extra chars, not sure why?
- //if (tempBuf0.length() > header->numFlowsPerRead) { tempBuf1 = tempBuf1.substr(0, header->numFlowsPerRead); strcpy(header->flowChars, tempBuf1.c_str()); }
- //in.read(buffer, header->numFlowsPerRead);
- //memcpy(header->flowChars, buffer, header->numFlowsPerRead);
- //delete[] buffer;
- //cout << "here" << endl;
- //string tempBuf1 = header->flowChars;
- //cout << "here " << in.tellg() << endl;
- //if (tempBuf1.length() > header->numFlowsPerRead) { tempBuf1 = tempBuf1.substr(0, header->numFlowsPerRead); strcpy(header->flowChars, tempBuf1.c_str()); }
+ char tempBuffer [header.numFlowsPerRead];
+ in.read(tempBuffer, header.numFlowsPerRead);
+ header.flowChars = tempBuffer;
+ if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead); }
- cout << "here " << header->flowChars << '\t' << in.tellg() << endl;
//read key
- //header->keyLength = 4;
- //char* myAlloc2 = new char(4); cout << "alloced" << endl;
- header->keySequence = new char(header->keyLength);
- //char* myAlloc = new char(4);
- cout << "here " << endl;
- in.read(header->keySequence, header->keyLength);
- string tempBuf2 = header->keySequence;
- if (tempBuf2.length() > header->keyLength) { tempBuf2 = tempBuf2.substr(0, header->keyLength); strcpy(header->keySequence, tempBuf2.c_str()); }
- cout << "here " << header->keySequence << '\t' << in.tellg() << endl;
-
+ char myAlloc [header.keyLength];
+ in.read(myAlloc, header.keyLength);
+ header.keySequence = myAlloc;
+ if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength); }
+
/* Pad to 8 chars */
int spotInFile = in.tellg();
- //cout << spotInFile << endl;
- int spot = floor((spotInFile + 7) /(float) 8) * 8;
- //cout << spot << endl;
+ int spot = (spotInFile + 7)& ~7;
in.seekg(spot);
-
- //exit(1);
-
+
}else{
m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
}
}
}
//**********************************************************************************************************************
-int SffInfoCommand::readHeader(ifstream& in, Header* header){
+int SffInfoCommand::readHeader(ifstream& in, Header& header){
try {
if (!in.eof()) {
- string tempBuf = "";
//read header length
- char* buffer = new char(sizeof(header->headerLength));
- in.read(buffer, sizeof(header->headerLength));
- header->headerLength = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer [sizeof(header.headerLength)];
+ in.read(buffer, sizeof(header.headerLength));
+ header.headerLength = be_int2(*(unsigned short *)(&buffer));
//read name length
- buffer = new char(sizeof(header->nameLength));
- in.read(buffer, sizeof(header->nameLength));
- header->nameLength = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer2 [sizeof(header.nameLength)];
+ in.read(buffer2, sizeof(header.nameLength));
+ header.nameLength = be_int2(*(unsigned short *)(&buffer2));
//read num bases
- buffer = new char(sizeof(header->numBases));
- in.read(buffer, sizeof(header->numBases));
- header->numBases = be_int4(*(unsigned int *)(buffer));
- delete[] buffer;
+ char buffer3 [sizeof(header.numBases)];
+ in.read(buffer3, sizeof(header.numBases));
+ header.numBases = be_int4(*(unsigned int *)(&buffer3));
//read clip qual left
- buffer = new char(sizeof(header->clipQualLeft));
- in.read(buffer, sizeof(header->clipQualLeft));
- header->clipQualLeft = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer4 [sizeof(header.clipQualLeft)];
+ in.read(buffer4, sizeof(header.clipQualLeft));
+ header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
//read clip qual right
- buffer = new char(sizeof(header->clipQualRight));
- in.read(buffer, sizeof(header->clipQualRight));
- header->clipQualRight = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer5 [sizeof(header.clipQualRight)];
+ in.read(buffer5, sizeof(header.clipQualRight));
+ header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
//read clipAdapterLeft
- buffer = new char(sizeof(header->clipAdapterLeft));
- in.read(buffer, sizeof(header->clipAdapterLeft));
- header->clipAdapterLeft = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer6 [sizeof(header.clipAdapterLeft)];
+ in.read(buffer6, sizeof(header.clipAdapterLeft));
+ header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
//read clipAdapterRight
- buffer = new char(sizeof(header->clipAdapterRight));
- in.read(buffer, sizeof(header->clipAdapterRight));
- header->clipAdapterRight = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer7 [sizeof(header.clipAdapterRight)];
+ in.read(buffer7, sizeof(header.clipAdapterRight));
+ header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
//read name
- header->name = new char(header->nameLength);
- //buffer = new char(header->nameLength);
- in.read(header->name, header->nameLength);
- //memcpy(header->name, buffer, header->nameLength);
- //delete[] buffer;
-
+ char tempBuffer [header.nameLength];
+ in.read(tempBuffer, header.nameLength);
+ header.name = tempBuffer;
+ if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); }
+
+ /* Pad to 8 chars */
+ int spotInFile = in.tellg();
+ int spot = (spotInFile + 7)& ~7;
+ in.seekg(spot);
+
}else{
m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
}
}
}
//**********************************************************************************************************************
-int SffInfoCommand::readSeqData(ifstream& in, seqRead* read, int numFlowReads, int numBases){
+int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
try {
if (!in.eof()) {
-
- string tempBuf = "";
- char* buffer;
-
+
//read flowgram
- read->flowgram.resize(numFlowReads);
+ read.flowgram.resize(numFlowReads);
for (int i = 0; i < numFlowReads; i++) {
- buffer = new char((sizeof(unsigned short)));
+ char buffer [sizeof(unsigned short)];
in.read(buffer, (sizeof(unsigned short)));
- read->flowgram[i] = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
}
//read flowIndex
- read->flowIndex.resize(numBases);
+ read.flowIndex.resize(numBases);
for (int i = 0; i < numBases; i++) {
- //buffer = new char(1);
- char temp;
- in.read(&temp, 1);
- read->flowgram[i] = be_int1(*(unsigned int *)(&temp));
- //delete[] buffer;
+ char temp[1];
+ in.read(temp, 1);
+ read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
}
//read bases
- read->bases = new char(numBases);
- in.read(read->bases, numBases);
- tempBuf = buffer;
- if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str()); }
+ char tempBuffer[numBases];
+ in.read(tempBuffer, numBases);
+ read.bases = tempBuffer;
+ if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases); }
//read flowgram
- read->qualScores.resize(numBases);
+ read.qualScores.resize(numBases);
for (int i = 0; i < numBases; i++) {
- char temp;
- in.read(&temp, 1);
- read->qualScores[i] = be_int1(*(unsigned int *)(&temp));
+ char temp[1];
+ in.read(temp, 1);
+ read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
}
/* Pad to 8 chars */
int spotInFile = in.tellg();
- cout << spotInFile << endl;
- int spot = floor((spotInFile + 7) /(float) 8) * 8;
- cout << spot << endl;
+ int spot = (spotInFile + 7)& ~7;
in.seekg(spot);
}else{
}
}
//**********************************************************************************************************************
-int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader* header, bool debug) {
+int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
try {
- string output = "Common Header:\nMagic Number: ";
- output += toString(header->magicNumber) + '\n';
- output += "Version: " + toString(header->version) + '\n';
- output += "Index Offset: " + toString(header->indexOffset) + '\n';
- output += "Index Length: " + toString(header->indexLength) + '\n';
- output += "Number of Reads: " + toString(header->numReads) + '\n';
- output += "Header Length: " + toString(header->headerLength) + '\n';
- output += "Key Length: " + toString(header->keyLength) + '\n';
- output += "Number of Flows: " + toString(header->numFlowsPerRead) + '\n';
- output += "Format Code: " + toString(header->flogramFormatCode) + '\n';
- output += "Flow Chars: " + toString(header->flowChars) + '\n';
- output += "Key Sequence: " + toString(header->keySequence) + '\n';
-
- out << output << endl;
-
- if (debug) { cout << output << endl; }
+ out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
+ out << "Version: " << header.version << endl;
+ out << "Index Offset: " << header.indexOffset << endl;
+ out << "Index Length: " << header.indexLength << endl;
+ out << "Number of Reads: " << header.numReads << endl;
+ out << "Header Length: " << header.headerLength << endl;
+ out << "Key Length: " << header.keyLength << endl;
+ out << "Number of Flows: " << header.numFlowsPerRead << endl;
+ out << "Format Code: " << header.flogramFormatCode << endl;
+ out << "Flow Chars: " << header.flowChars << endl;
+ out << "Key Sequence: " << header.keySequence << endl << endl;
return 0;
}
}
}
//**********************************************************************************************************************
-int SffInfoCommand::printHeader(ofstream& out, Header* header, bool debug) {
+int SffInfoCommand::printHeader(ofstream& out, Header& header) {
try {
- string name = header->name;
- string output = ">" + name + "\nRead Header Length: " + toString(header->headerLength) + '\n';
- output += "Name Length: " + toString(header->nameLength) + '\n';
- output += "Number of Bases: " + toString(header->numBases) + '\n';
- output += "Clip Qual Left: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Qual Right: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Adap Left: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Adap Right: " + toString(header->clipQualLeft) + '\n';
-
- out << output << endl;
+ out << ">" << header.name << endl;
+ out << "Read Header Length: " << header.headerLength << endl;
+ out << "Name Length: " << header.nameLength << endl;
+ out << "Number of Bases: " << header.numBases << endl;
+ out << "Clip Qual Left: " << header.clipQualLeft << endl;
+ out << "Clip Qual Right: " << header.clipQualRight << endl;
+ out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
+ out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
- if (debug) { cout << output << endl; }
-
return 0;
}
catch(exception& e) {
}
//**********************************************************************************************************************
-int SffInfoCommand::printSeqData(ofstream& out, seqRead* read, bool debug) {
+int SffInfoCommand::printSeqData(ofstream& out, seqRead& read) {
try {
-
- string output = "FlowGram: ";
- for (int i = 0; i < read->flowgram.size(); i++) { output += toString(read->flowgram[i]) +'\t'; }
- output += "\nFlow Indexes: ";
- for (int i = 0; i < read->flowIndex.size(); i++) { output += toString(read->flowIndex[i]) +'\t'; }
- string bases = read->bases;
- output += "\nBases: " + bases + '\n';
- for (int i = 0; i < read->qualScores.size(); i++) { output += toString(read->qualScores[i]) +'\t'; }
- output += '\n';
- out << output << endl;
+ out << "FlowGram: ";
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
+
+ out << endl << "Flow Indexes: ";
+ int sum = 0;
+ for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
- if (debug) { cout << output << endl; }
+ out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
+ for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ out << endl << endl;
return 0;
}
projects / mothur.git / commitdiff