- cout << endl;
- cout << "\t\tStart\tEnd\tNBases\tAmbigs\tPolymer" << endl;
- cout << "Minimum:\t" << startPosition[0] << '\t' << endPosition[0] << '\t' << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl;
- cout << "2.5%-tile:\t" << startPosition[ptile0_25] << '\t' << endPosition[ptile0_25] << '\t' << seqLength[ptile0_25] << '\t' << ambigBases[ptile0_25] << '\t' << longHomoPolymer[ptile0_25] << endl;
- cout << "25%-tile:\t" << startPosition[ptile25] << '\t' << endPosition[ptile25] << '\t' << seqLength[ptile25] << '\t' << ambigBases[ptile25] << '\t' << longHomoPolymer[ptile25] << endl;
- cout << "Median: \t" << startPosition[ptile50] << '\t' << endPosition[ptile50] << '\t' << seqLength[ptile50] << '\t' << ambigBases[ptile50] << '\t' << longHomoPolymer[ptile50] << endl;
- cout << "75%-tile:\t" << startPosition[ptile75] << '\t' << endPosition[ptile75] << '\t' << seqLength[ptile75] << '\t' << ambigBases[ptile75] << '\t' << longHomoPolymer[ptile75] << endl;
- cout << "97.5%-tile:\t" << startPosition[ptile97_5] << '\t' << endPosition[ptile97_5] << '\t' << seqLength[ptile97_5] << '\t' << ambigBases[ptile97_5] << '\t' << longHomoPolymer[ptile97_5] << endl;
- cout << "Maximum:\t" << startPosition[ptile100] << '\t' << endPosition[ptile100] << '\t' << seqLength[ptile100] << '\t' << ambigBases[ptile100] << '\t' << longHomoPolymer[ptile100] << endl;
- cout << "# of Seqs:\t" << numSeqs << endl;
+ //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
+ if (startPosition[0] == -1) { startPosition[0] = 0; }
+ if (endPosition[0] == -1) { endPosition[0] = 0; }
+
+ if (m->control_pressed) { outSummary.close(); remove(summaryFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); 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])); 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])); 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])); 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])); 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])); 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])); 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])); m->mothurOutEndLine();
+ m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
+
+ outSummary.close();