+double RefChimeraTest::alignQueryToReferences(string query, string reference, string& qAlign, string& rAlign, double& length){
+
+
+ try {
+ double GAP = -5;
+ double MATCH = 1;
+ double MISMATCH = -1;
+
+ int queryLength = query.length();
+ int refLength = reference.length();
+
+ vector<vector<double> > alignMatrix(queryLength + 1);
+ vector<vector<char> > alignMoves(queryLength + 1);
+
+ for(int i=0;i<=queryLength;i++){
+ if (m->control_pressed) { return 0; }
+ alignMatrix[i].resize(refLength + 1, 0);
+ alignMoves[i].resize(refLength + 1, 'x');
+ }
+
+ for(int i=0;i<=queryLength;i++){
+ if (m->control_pressed) { return 0; }
+ alignMatrix[i][0] = 0;//GAP * i;
+ alignMoves[i][0] = 'u';
+ }
+
+ for(int i=0;i<=refLength;i++){
+ if (m->control_pressed) { return 0; }
+ alignMatrix[0][i] = 0;//GAP * i;
+ alignMoves[0][i] = 'l';
+ }
+
+ for(int i=1;i<=queryLength;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ for(int j=1;j<=refLength;j++){
+
+ double nogapScore;
+ if(query[i-1] == reference[j-1]){ nogapScore = alignMatrix[i-1][j-1] + MATCH; }
+ else { nogapScore = alignMatrix[i-1][j-1] + MISMATCH; }
+
+ double leftScore;
+ if(i == queryLength) { leftScore = alignMatrix[i][j-1]; }
+ else { leftScore = alignMatrix[i][j-1] + GAP; }
+
+
+ double upScore;
+ if(j == refLength) { upScore = alignMatrix[i-1][j]; }
+ else { upScore = alignMatrix[i-1][j] + GAP; }
+
+ if(nogapScore > leftScore){
+ if(nogapScore > upScore){
+ alignMoves[i][j] = 'd';
+ alignMatrix[i][j] = nogapScore;
+ }
+ else{
+ alignMoves[i][j] = 'u';
+ alignMatrix[i][j] = upScore;
+ }
+ }
+ else{
+ if(leftScore > upScore){
+ alignMoves[i][j] = 'l';
+ alignMatrix[i][j] = leftScore;
+ }
+ else{
+ alignMoves[i][j] = 'u';
+ alignMatrix[i][j] = upScore;
+ }
+ }
+ }
+ }
+
+ int end = refLength - 1;
+ int maxRow = 0;
+ double maxRowValue = -2147483647;
+ for(int i=0;i<queryLength;i++){
+ if(alignMatrix[i][end] > maxRowValue){
+ maxRow = i;
+ maxRowValue = alignMatrix[i][end];
+ }
+ }
+
+ end = queryLength - 1;
+ int maxColumn = 0;
+ double maxColumnValue = -2147483647;
+
+ for(int j=0;j<refLength;j++){
+ if(alignMatrix[end][j] > maxColumnValue){
+ maxColumn = j;
+ maxColumnValue = alignMatrix[end][j];
+ }
+ }
+
+ int row = queryLength-1;
+ int column = refLength-1;
+
+ if(maxColumn == column && maxRow == row){} // if the max values are the lower right corner, then we're good
+ else if(alignMatrix[row][maxColumn] < alignMatrix[maxRow][column]){
+ for(int i=maxRow+1;i<queryLength;i++){ // decide whether sequence A or B needs the gaps at the end either set
+ alignMoves[i][column] = 'u';// the pointer upwards or...
+ }
+
+ }
+ else {
+ for(int i=maxColumn+1;i<refLength;i++){
+ alignMoves[row][i] = 'l'; // ...to the left
+ }
+ }
+
+ int i = queryLength;
+ int j = refLength;
+
+
+ qAlign = "";
+ rAlign = "";
+
+ int diffs = 0;
+ length = 0;
+
+ while(i > 0 && j > 0){
+
+ if (m->control_pressed) { return 0; }
+
+ if(alignMoves[i][j] == 'd'){
+ qAlign = query[i-1] + qAlign;
+ rAlign = reference[j-1] + rAlign;
+
+ if(query[i-1] != reference[j-1]){ diffs++; }
+ length++;
+
+ i--;
+ j--;
+ }
+ else if(alignMoves[i][j] == 'u'){
+ qAlign = query[i-1] + qAlign;
+
+ if(j != refLength) { rAlign = '-' + rAlign; diffs++; length++; }
+ else { rAlign = '.' + rAlign; }
+ i--;
+ }
+ else if(alignMoves[i][j] == 'l'){
+ rAlign = reference[j-1] + rAlign;
+
+ if(i != queryLength){ qAlign = '-' + qAlign; diffs++; length++; }
+ else { qAlign = '.' + qAlign; }
+ j--;
+ }
+ }
+
+ if(i>0){
+ qAlign = query.substr(0, i) + qAlign;
+ rAlign = string(i, '.') + rAlign;
+ }
+ else if(j>0){
+ qAlign = string(j, '.') + qAlign;
+ rAlign = reference.substr(0, j) + rAlign;
+ }
+
+
+ return diffs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RefChimeraTest", "alignQueryToReferences");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int RefChimeraTest::getUnalignedDiffs(string qAlign, string rAlign, vector<int>& leftDiffs, vector<int>& leftMap, vector<int>& rightDiffs, vector<int>& rightMap){
+ try {
+ int alignLength = qAlign.length();
+
+ int lDiffs = 0;
+ int lCount = 0;
+ for(int l=0;l<alignLength;l++){
+
+ if (m->control_pressed) { return 0; }
+
+ if(qAlign[l] == '-'){
+ lDiffs++;
+ }
+ else if(qAlign[l] != '.'){
+
+ if(rAlign[l] == '-'){
+ lDiffs++;
+ }
+ else if(qAlign[l] != rAlign[l]){;// && rAlign[l] != '.'){
+ lDiffs++;
+ }
+ leftDiffs[lCount] = lDiffs;
+ leftMap[lCount] = l;
+
+ lCount++;
+ }
+ }
+
+ int rDiffs = 0;
+ int rCount = 0;
+ for(int l=alignLength-1;l>=0;l--){
+
+ if (m->control_pressed) { return 0; }
+
+ if(qAlign[l] == '-'){
+ rDiffs++;
+ }
+ else if(qAlign[l] != '.'){
+
+ if(rAlign[l] == '-'){
+ rDiffs++;
+ }
+ else if(qAlign[l] != rAlign[l]){;// && rAlign[l] != '.'){
+ rDiffs++;
+ }
+
+ rightDiffs[rCount] = rDiffs;
+ rightMap[rCount] = l;
+ rCount++;
+ }
+
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RefChimeraTest", "getUnalignedDiffs");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int RefChimeraTest::getAlignedMismatches(string& querySeq, vector<vector<int> >& left, vector<vector<int> >& right, int& bestRefSeq){