+
+bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
+ try {
+ bool success = 1;
+ int length = oligo.length();
+
+ for(int i=0;i<length;i++){
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+
+ if(success == 0) { break; }
+ }
+ else{
+ success = 1;
+ }
+ }
+
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+ exit(1);
+ }
+
+}
+//***************************************************************************************************************
+
+int TrimSeqsCommand::countDiffs(string oligo, string seq){
+ try {
+
+ int length = oligo.length();
+ int countDiffs = 0;
+
+ for(int i=0;i<length;i++){
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+
+ }
+ }
+
+ return countDiffs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "countDiffs");
+ exit(1);
+ }
+
+}
+//***************************************************************************************************************
+
+//bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
+// try {
+//
+// string rawSequence = seq.getUnaligned();
+// int seqLength = seq.getNumBases();
+// bool success = 0; //guilty until proven innocent
+// string name;
+//
+// qFile >> name;
+// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
+//
+// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
+//
+// int score;
+// int end = seqLength;
+//
+// for(int i=0;i<seqLength;i++){
+// qFile >> score;
+//
+// if(score < qThreshold){
+// end = i;
+// break;
+// }
+// }
+// for(int i=end+1;i<seqLength;i++){
+// qFile >> score;
+// }
+//
+// seq.setUnaligned(rawSequence.substr(0,end));
+//
+// return 1;
+// }
+// catch(exception& e) {
+// m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+// exit(1);
+// }
+//}
+
+//***************************************************************************************************************
+
+//bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
+// try {
+// string rawSequence = seq.getUnaligned();
+// int seqLength = seq.getNumBases();
+// bool success = 0; //guilty until proven innocent
+// string name;
+//
+// qFile >> name;
+// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
+//
+// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
+//
+// float score;
+// float average = 0;
+//
+// for(int i=0;i<seqLength;i++){
+// qFile >> score;
+// average += score;
+// }
+// average /= seqLength;
+//
+// if(average >= qAverage) { success = 1; }
+// else { success = 0; }
+//
+// return success;
+// }
+// catch(exception& e) {
+// m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+// exit(1);
+// }
+//}
+
+//***************************************************************************************************************