+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
+ m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine();
+ m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine();
+ m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine();
+ m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine();
+ m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
+ m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
+ m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
+ m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
+
+ if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
+ else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
+
+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
+ m->mothurOutEndLine();
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
+ try {
+
+ ofstream outSummary;
+ m->openOutputFile(sumFile, outSummary);
+
+ //print header if you are process 0
+ if (filePos->start == 0) {
+ outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
+ }
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
+
+ Sequence current(in); m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(current.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ startPosition.push_back(current.getStartPos());
+ endPosition.push_back(current.getEndPos());
+ seqLength.push_back(current.getNumBases());
+ ambigBases.push_back(current.getAmbigBases());
+ longHomoPolymer.push_back(current.getLongHomoPolymer());
+ }
+
+ count++;
+ outSummary << current.getName() << '\t';
+ outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+ outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+ outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+ if (in.eof()) { break; }
+ #endif
+
+ //report progress
+ //if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ }
+ //report progress
+ //if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
+ exit(1);
+ }
+}
+#ifdef USE_MPI
+/**************************************************************************************/
+int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
+ try {
+
+ int pid;
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
+
+ Sequence current(iss);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(current.getName());
+
+ if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ startPosition.push_back(current.getStartPos());
+ endPosition.push_back(current.getEndPos());
+ seqLength.push_back(current.getNumBases());
+ ambigBases.push_back(current.getAmbigBases());
+ longHomoPolymer.push_back(current.getLongHomoPolymer());
+ }
+
+ string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
+ outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
+
+ //output to file
+ length = outputString.length();
+ char* buf3 = new char[length];
+ memcpy(buf3, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
+ delete buf3;
+ }
+ }
+