- //map query sequences to their most similiar sequences in the template - Parallelized
- mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
- if (processors == 1) { findPairs(lines[0]->start, lines[0]->end); }
- else { createProcessesPairs(); }
- mothurOut("Done."); mothurOutEndLine();
- // itBest = bestfit.begin();
- // itBest++; itBest++;
-//cout << itBest->first->getName() << '\t' << itBest->second->getName() << endl;
- //find Oqs for each sequence - the observed distance in each window - Parallelized
- mothurOut("Calculating observed percentage differences for each sequence... "); cout.flush();
- if (processors == 1) { calcObserved(lines[0]->start, lines[0]->end); }
- else { createProcessesObserved(); }
- mothurOut("Done."); mothurOutEndLine();
+ distcalculator = new ignoreGaps();
+
+
+ if (processors == 1) {
+ mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
+ bestfit = findPairs(lines[0]->start, lines[0]->end);
+
+ //ex.align matches from wigeon
+/*for (int m = 0; m < templateSeqs.size(); m++) {
+ if (templateSeqs[m]->getName() == "159481") { bestfit[17] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "100137") { bestfit[16] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "112956") { bestfit[15] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "102326") { bestfit[14] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "66229") { bestfit[13] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "206276") { bestfit[12] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "63607") { bestfit[11] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "7056") { bestfit[10] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "7088") { bestfit[9] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "17553") { bestfit[8] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "131723") { bestfit[7] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "69013") { bestfit[6] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "24543") { bestfit[5] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "27824") { bestfit[4] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "1456") { bestfit[3] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "1456") { bestfit[2] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "141312") { bestfit[1] = *(templateSeqs[m]); }
+ if (templateSeqs[m]->getName() == "141312") { bestfit[0] = *(templateSeqs[m]); }
+
+
+}*/
+
+ for (int j = 0; j < bestfit.size(); j++) {
+ //chops off beginning and end of sequences so they both start and end with a base
+ trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
+ }
+ mothurOut("Done."); mothurOutEndLine();
+
+ mothurOut("Finding window breaks... "); cout.flush();
+ for (int i = lines[0]->start; i < lines[0]->end; i++) {
+ it = trimmed[i].begin();
+cout << "trimmed = " << it->first << '\t' << it->second << endl;
+ vector<int> win = findWindows(querySeqs[i], it->first, it->second, windowSizes[i]);
+ windowsForeachQuery[i] = win;
+ }
+ mothurOut("Done."); mothurOutEndLine();