--- /dev/null
+/*
+ * maligner.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/23/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "maligner.h"
+
+/***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight
+Maligner::Maligner(vector<Sequence> temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) {
+ //numWanted(num), , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight)
+
+ m = MothurOut::getInstance();
+
+}
+/***********************************************************************/
+string Maligner::getResults(Sequence q, DeCalculator decalc) {
+ try {
+
+ outputResults.clear();
+
+ //make copy so trimming doesn't destroy query from calling class - remember to deallocate
+ query.setName(q.getName()); query.setAligned(q.getAligned());
+
+ string chimera;
+
+ //copy refSeqs so that filter does not effect original
+ for(int i = 0; i < db.size(); i++) {
+ Sequence newSeq(db[i].getName(), db[i].getAligned());
+ refSeqs.push_back(newSeq);
+ }
+
+ refSeqs = minCoverageFilter(refSeqs);
+
+ if (refSeqs.size() < 2) {
+ //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
+ percentIdenticalQueryChimera = 0.0;
+ return "unknown";
+ }
+
+ int chimeraPenalty = computeChimeraPenalty();
+
+ //fills outputResults
+ chimera = chimeraMaligner(chimeraPenalty, decalc);
+
+ if (m->control_pressed) { return chimera; }
+
+ //free memory
+ //delete query;
+
+ //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
+
+ return chimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "getResults");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator decalc) {
+ try {
+
+ string chimera;
+ //trims seqs to first non gap char in all seqs and last non gap char in all seqs
+ spotMap = decalc.trimSeqs(query, refSeqs);
+
+ //you trimmed the whole sequence, skip
+ if (query.getAligned() == "") { return "no"; }
+
+ vector<Sequence> temp = refSeqs;
+ temp.push_back(query);
+
+ temp = verticalFilter(temp);
+ query = temp[temp.size()-1];
+ for (int i = 0; i < temp.size()-1; i++) { refSeqs[i] = temp[i]; }
+
+ //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl ; }//<< refSeqs[i]->getAligned() << endl
+
+ vector< vector<score_struct> > matrix = buildScoreMatrix(query.getAligned().length(), refSeqs.size()); //builds and initializes
+
+ if (m->control_pressed) { return chimera; }
+
+ fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
+
+ vector<score_struct> path = extractHighestPath(matrix);
+
+ if (m->control_pressed) { return chimera; }
+
+ vector<trace_struct> trace = mapTraceRegionsToAlignment(path);
+
+ if (trace.size() > 1) { chimera = "yes"; }
+ else { chimera = "no"; return chimera; }
+
+ int traceStart = path[0].col;
+ int traceEnd = path[path.size()-1].col;
+ string queryInRange = query.getAligned();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+// cout << queryInRange << endl;
+ string chimeraSeq = constructChimericSeq(trace, refSeqs);
+// cout << chimeraSeq << endl;
+
+// cout << queryInRange.length() << endl;
+// cout << chimeraSeq.length() << endl;
+
+ percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
+
+// cout << percentIdenticalQueryChimera << endl;
+ /*
+ vector<trace_struct> trace = extractHighestPath(matrix);
+
+ //cout << "traces\n";
+ //for(int i=0;i<trace.size();i++){
+ // cout << trace[i].col << '\t' << trace[i].oldCol << '\t' << refSeqs[trace[i].row]->getName() << endl;
+ //}
+
+ if (trace.size() > 1) { chimera = "yes"; }
+ else { chimera = "no"; return chimera; }
+
+ int traceStart = trace[0].col;
+ int traceEnd = trace[trace.size()-1].oldCol;
+ string queryInRange = query->getAligned();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/
+
+ if (m->control_pressed) { return chimera; }
+
+ //save output results
+ for (int i = 0; i < trace.size(); i++) {
+ int regionStart = trace[i].col;
+ int regionEnd = trace[i].oldCol;
+ int seqIndex = trace[i].row;
+
+// cout << regionStart << '\t' << regionEnd << '\t' << seqIndex << endl;
+ results temp;
+
+ temp.parent = refSeqs[seqIndex].getName();
+ temp.parentAligned = db[seqIndex].getAligned();
+ temp.nastRegionStart = spotMap[regionStart];
+ temp.nastRegionEnd = spotMap[regionEnd];
+ temp.regionStart = unalignedMap[regionStart];
+ temp.regionEnd = unalignedMap[regionEnd];
+
+ string parentInRange = refSeqs[seqIndex].getAligned();
+ parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1));
+
+ temp.queryToParent = computePercentID(queryInRange, parentInRange);
+ temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
+
+ string queryInRegion = query.getAligned();
+ queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1));
+
+ string parentInRegion = refSeqs[seqIndex].getAligned();
+ parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1));
+
+ temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
+
+ //cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " << temp.divR << endl;
+
+ outputResults.push_back(temp);
+ }
+
+ return chimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "chimeraMaligner");
+ exit(1);
+ }
+}
+/***********************************************************************/
+//removes top matches that do not have minimum coverage with query.
+vector<Sequence> Maligner::minCoverageFilter(vector<Sequence> ref){
+ try {
+ vector<Sequence> newRefs;
+
+ string queryAligned = query.getAligned();
+
+ for (int i = 0; i < ref.size(); i++) {
+
+ string refAligned = ref[i].getAligned();
+
+ int numBases = 0;
+ int numCovered = 0;
+
+ //calculate coverage
+ for (int j = 0; j < queryAligned.length(); j++) {
+
+ if (isalpha(queryAligned[j])) {
+ numBases++;
+
+ if (isalpha(refAligned[j])) {
+ numCovered++;
+ }
+ }
+ }
+
+ int coverage = ((numCovered/(float)numBases)*100);
+
+ //if coverage above minimum
+ if (coverage > minCoverage) {
+ newRefs.push_back(ref[i]);
+ }//else {
+ //delete ref[i];
+ //}
+ }
+
+ return newRefs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "minCoverageFilter");
+ exit(1);
+ }
+}
+/***********************************************************************/
+// a breakpoint should yield fewer mismatches than this number with respect to the best parent sequence.
+int Maligner::computeChimeraPenalty() {
+ try {
+
+ int numAllowable = ((1.0 - (1.0/minDivR)) * query.getNumBases());
+
+// if(numAllowable < 1){ numAllowable = 1; }
+
+ int penalty = int(numAllowable + 1) * misMatchPenalty;
+
+ return penalty;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "computeChimeraPenalty");
+ exit(1);
+ }
+}
+/***********************************************************************/
+//this is a vertical filter
+vector<Sequence> Maligner::verticalFilter(vector<Sequence> seqs) {
+ try {
+ vector<int> gaps; gaps.resize(query.getAligned().length(), 0);
+
+ string filterString = (string(query.getAligned().length(), '1'));
+
+ //for each sequence
+ for (int i = 0; i < seqs.size(); i++) {
+
+ string seqAligned = seqs[i].getAligned();
+
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is a gap
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
+ }
+ }
+
+ //zero out spot where all sequences have blanks
+ int numColRemoved = 0;
+ for(int i = 0; i < seqs[0].getAligned().length(); i++){
+ if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
+ }
+
+ map<int, int> newMap;
+ //for each sequence
+ for (int i = 0; i < seqs.size(); i++) {
+
+ string seqAligned = seqs[i].getAligned();
+ string newAligned = "";
+ int count = 0;
+
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //if this spot is not a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ newMap[count] = spotMap[j];
+ count++;
+ }
+ }
+
+ seqs[i].setAligned(newAligned);
+ }
+
+ string query = seqs[seqs.size()-1].getAligned();
+ int queryLength = query.length();
+
+ unalignedMap.resize(queryLength, 0);
+
+
+ for(int i=1;i<queryLength;i++){
+ if(query[i] != '.' && query[i] != '-'){
+ unalignedMap[i] = unalignedMap[i-1] + 1;
+ }
+ else{
+ unalignedMap[i] = unalignedMap[i-1];
+ }
+ }
+
+ spotMap = newMap;
+
+ return seqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "verticalFilter");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector< vector<score_struct> > Maligner::buildScoreMatrix(int cols, int rows) {
+ try{
+
+ vector< vector<score_struct> > m(rows);
+
+ for (int i = 0; i < rows; i++) {
+ for (int j = 0; j < cols; j++) {
+
+ //initialize each cell
+ score_struct temp;
+ temp.prev = -1;
+ temp.score = -9999999;
+ temp.col = j;
+ temp.row = i;
+
+ m[i].push_back(temp);
+ }
+ }
+
+ return m;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "buildScoreMatrix");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence> seqs, int penalty) {
+ try{
+
+ //get matrix dimensions
+ int numCols = query.getAligned().length();
+ int numRows = seqs.size();
+
+// cout << numRows << endl;
+
+ //initialize first col
+ string queryAligned = query.getAligned();
+ for (int i = 0; i < numRows; i++) {
+ string subjectAligned = seqs[i].getAligned();
+
+ //are you both gaps?
+ if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
+ ms[i][0].score = 0;
+// ms[i][0].mismatches = 0;
+ }else if (queryAligned[0] == subjectAligned[0]) { //|| subjectAligned[0] == 'N')
+ ms[i][0].score = matchScore;
+// ms[i][0].mismatches = 0;
+ }else{
+ ms[i][0].score = 0;
+// ms[i][0].mismatches = 1;
+ }
+ }
+
+ //fill rest of matrix
+ for (int j = 1; j < numCols; j++) { //iterate through matrix columns
+
+// for (int i = 0; i < 1; i++) { //iterate through matrix rows
+ for (int i = 0; i < numRows; i++) { //iterate through matrix rows
+
+ string subjectAligned = seqs[i].getAligned();
+
+ int matchMisMatchScore = 0;
+ //are you both gaps?
+ if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
+ //leave the same
+ }else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
+ //leave the same
+ }else if (queryAligned[j] == subjectAligned[j]) {
+ matchMisMatchScore = matchScore;
+ }else if (queryAligned[j] != subjectAligned[j]) {
+ matchMisMatchScore = misMatchPenalty;
+ }
+
+ //compute score based on previous columns scores
+ for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
+
+ int sumScore = matchMisMatchScore + ms[prevIndex][j-1].score;
+
+ //you are not at yourself
+ if (prevIndex != i) { sumScore += penalty; }
+ if (sumScore < 0) { sumScore = 0; }
+
+ if (sumScore > ms[i][j].score) {
+ ms[i][j].score = sumScore;
+ ms[i][j].prev = prevIndex;
+ }
+ }
+// cout << i << '\t' << j << '\t' << queryAligned[j] << '\t' << subjectAligned[j] << '\t' << matchMisMatchScore << '\t' << ms[i][j].score << endl;
+
+ }
+
+ }
+
+
+
+
+
+// cout << numRows << '\t' << numCols << endl;
+// for(int i=0;i<numRows;i++){
+// cout << seqs[i]->getName();
+// for(int j=0;j<numCols;j++){
+// cout << '\t' << ms[i][j].score;
+// }
+// cout << endl;
+// }
+// cout << endl;
+//
+// for(int i=0;i<numRows;i++){
+// cout << seqs[i]->getName();
+// for(int j=0;j<numCols;j++){
+// cout << '\t' << ms[i][j].prev;
+// }
+// cout << endl;
+// }
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "fillScoreMatrix");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
+ try {
+
+ //get matrix dimensions
+ int numCols = query.getAligned().length();
+ int numRows = ms.size();
+
+
+ //find highest score scoring matrix
+ score_struct highestStruct;
+ int highestScore = 0;
+
+ for (int i = 0; i < numRows; i++) {
+ for (int j = 0; j < numCols; j++) {
+ if (ms[i][j].score > highestScore) {
+ highestScore = ms[i][j].score;
+ highestStruct = ms[i][j];
+ }
+ }
+ }
+
+ vector<score_struct> path;
+
+ int rowIndex = highestStruct.row;
+ int pos = highestStruct.col;
+ int score = highestStruct.score;
+
+// cout << rowIndex << '\t' << pos << '\t' << score << endl;
+
+ while (pos >= 0 && score > 0) {
+ score_struct temp = ms[rowIndex][pos];
+ score = temp.score;
+
+ if (score > 0) { path.push_back(temp); }
+
+ rowIndex = temp.prev;
+ pos--;
+ }
+
+ reverse(path.begin(), path.end());
+
+ return path;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "extractHighestPath");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path) {
+ try {
+ vector<trace_struct> trace;
+
+ int region_index = path[0].row;
+ int region_start = path[0].col;
+
+ for (int i = 1; i < path.size(); i++) {
+
+ int next_region_index = path[i].row;
+ //cout << i << '\t' << next_region_index << endl;
+
+ if (next_region_index != region_index) {
+
+ // add trace region
+ int col_index = path[i].col;
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = col_index-1;
+ temp.row = region_index;
+
+ trace.push_back(temp);
+
+ region_index = path[i].row;
+ region_start = col_index;
+ }
+ }
+
+ // get last one
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = path[path.size()-1].col;
+ temp.row = region_index;
+ trace.push_back(temp);
+
+ return trace;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
+ exit(1);
+ }
+}
+
+/***************************************************************************************************************
+
+vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
+ try {
+
+
+ //get matrix dimensions
+ int numCols = query->getAligned().length();
+ int numRows = ms.size();
+
+
+ //find highest score scoring matrix
+ vector<score_struct> highestStruct;
+ int highestScore = 0;
+
+ for (int i = 0; i < numRows; i++) {
+ for (int j = 0; j < numCols; j++) {
+ if (ms[i][j].score > highestScore) {
+ highestScore = ms[i][j].score;
+ highestStruct.resize(0);
+ highestStruct.push_back(ms[i][j]);
+ }
+ else if(ms[i][j].score == highestScore){
+ highestStruct.push_back(ms[i][j]);
+ }
+ }
+ }
+
+ //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;
+
+ vector<trace_struct> maxTrace;
+ double maxPercentIdenticalQueryAntiChimera = 0;
+
+ for(int i=0;i<highestStruct.size();i++){
+
+ vector<score_struct> path;
+
+ int rowIndex = highestStruct[i].row;
+ int pos = highestStruct[i].col;
+ int score = highestStruct[i].score;
+
+ while (pos >= 0 && score > 0) {
+ score_struct temp = ms[rowIndex][pos];
+ score = temp.score;
+
+ if (score > 0) { path.push_back(temp); }
+
+ rowIndex = temp.prev;
+ pos--;
+ }
+
+ reverse(path.begin(), path.end());
+
+ vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
+
+ //cout << "traces\n";
+ //for(int j=0;j<trace.size();j++){
+ // cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
+ //}
+
+ int traceStart = path[0].col;
+ int traceEnd = path[path.size()-1].col;
+// cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
+
+ string queryInRange = query->getAligned();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+// cout << "here" << endl;
+ string chimeraSeq = constructChimericSeq(trace, refSeqs);
+ string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
+
+ percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
+ double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
+// cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
+
+ if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
+ maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
+ maxTrace = trace;
+ }
+ }
+// cout << maxPercentIdenticalQueryAntiChimera << endl;
+ return maxTrace;
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "extractHighestPath");
+ exit(1);
+ }
+}
+
+***************************************************************************************************************
+
+vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
+ try {
+ vector<trace_struct> trace;
+
+ int region_index = path[0].row;
+ int region_start = path[0].col;
+
+ for (int i = 1; i < path.size(); i++) {
+
+ int next_region_index = path[i].row;
+
+ if (next_region_index != region_index) {
+
+ // add trace region
+ int col_index = path[i].col;
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = col_index-1;
+ temp.row = region_index;
+
+ trace.push_back(temp);
+
+ region_index = path[i].row;
+ region_start = col_index;
+ }
+ }
+
+ // get last one
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = path[path.size()-1].col;
+ temp.row = region_index;
+ trace.push_back(temp);
+
+// cout << endl;
+// cout << trace.size() << endl;
+// for(int i=0;i<trace.size();i++){
+// cout << seqs[trace[i].row]->getName() << endl;
+// }
+// cout << endl;
+
+ return trace;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
+ exit(1);
+ }
+}
+*/
+//***************************************************************************************************************
+
+string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence> seqs) {
+ try {
+ string chimera = "";
+
+ for (int i = 0; i < trace.size(); i++) {
+// cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
+
+ string seqAlign = seqs[trace[i].row].getAligned();
+ seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
+ chimera += seqAlign;
+ }
+// cout << chimera << endl;
+// if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); } //this was introducing a fence post error
+// cout << chimera << endl;
+ return chimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "constructChimericSeq");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence> seqs) {
+ try {
+ string antiChimera = "";
+
+ for (int i = 0; i < trace.size(); i++) {
+// cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
+
+ int oppositeIndex = trace.size() - i - 1;
+
+ string seqAlign = seqs[trace[oppositeIndex].row].getAligned();
+ seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
+ antiChimera += seqAlign;
+ }
+
+ return antiChimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "constructChimericSeq");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+float Maligner::computePercentID(string queryAlign, string chimera) {
+ try {
+
+ if (queryAlign.length() != chimera.length()) {
+ m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
+ m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine();
+ m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
+ return -1.0;
+ }
+
+// cout << queryAlign.length() << endl;
+ int numIdentical = 0;
+ int countA = 0;
+ int countB = 0;
+ for (int i = 0; i < queryAlign.length(); i++) {
+ if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+ ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+ else {
+
+ bool charA = false; bool charB = false;
+ if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+ if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+
+
+ if (charA || charB) {
+
+ if (charA) { countA++; }
+ if (charB) { countB++; }
+
+ if (queryAlign[i] == chimera[i]) {
+ numIdentical++;
+ }
+ }
+// cout << queryAlign[i] << '\t' << chimera[i] << '\t' << countA << '\t' << countB << endl;
+
+ }
+ }
+
+// cout << "pat\t" << countA << '\t' << countB << '\t' << numIdentical << endl;
+
+
+ float numBases = (countA + countB) /(float) 2;
+
+ if (numBases == 0) { return 0; }
+
+// cout << numIdentical << '\t' << numBases << endl;
+
+ float percentIdentical = (numIdentical/(float)numBases) * 100;
+
+// cout << percentIdentical << endl;
+
+ return percentIdentical;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "computePercentID");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
projects / mothur.git / blobdiff