paralellized trim.seqs for windows. fixed bug in trim.flows that stopped fasta data...

[mothur.git] / trimoligos.cpp

diff --git a/trimoligos.cpp b/trimoligos.cpp
index cf818707c672c82acfdbd3bf896c9c0c2edbae36..8c523ce68d8a042bb702900d468def2aadad157b 100644 (file)
--- a/trimoligos.cpp
+++ b/trimoligos.cpp
@@ -576,13 +576,13 @@ bool TrimOligos::stripReverse(Sequence& seq){
 bool TrimOligos::stripLinker(Sequence& seq, QualityScores& qual){
        try {
                string rawSequence = seq.getUnaligned();
-               bool success = 0;       //guilty until proven innocent
+               bool success = ldiffs + 1;      //guilty until proven innocent
                
                for(int i=0;i<linker.size();i++){
                        string oligo = linker[i];
                        
                        if(rawSequence.length() < oligo.length()){
-                               success = 0;
+                               success = ldiffs + 10;
                                break;
                        }
                        
@@ -591,7 +591,7 @@ bool TrimOligos::stripLinker(Sequence& seq, QualityScores& qual){
                                if(qual.getName() != ""){
                                        qual.trimQScores(oligo.length(), -1);
                                }
-                               success = 1;
+                               success = 0;
                                break;
                        }
                }
@@ -688,19 +688,19 @@ bool TrimOligos::stripLinker(Sequence& seq){
        try {
                
                string rawSequence = seq.getUnaligned();
-               bool success = 0;       //guilty until proven innocent
+               bool success = ldiffs +1;       //guilty until proven innocent
                
                for(int i=0;i<linker.size();i++){
                        string oligo = linker[i];
                        
                        if(rawSequence.length() < oligo.length()){
-                               success = 0;
+                               success = ldiffs +10;
                                break;
                        }
                        
                        if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
                                seq.setUnaligned(rawSequence.substr(oligo.length()));
-                               success = 1;
+                               success = 0;
                                break;
                        }
                }       
@@ -792,13 +792,13 @@ bool TrimOligos::stripLinker(Sequence& seq){
 bool TrimOligos::stripSpacer(Sequence& seq, QualityScores& qual){
        try {
                string rawSequence = seq.getUnaligned();
-               bool success = 0;       //guilty until proven innocent
+               bool success = sdiffs+1;        //guilty until proven innocent
                
                for(int i=0;i<spacer.size();i++){
                        string oligo = spacer[i];
                        
                        if(rawSequence.length() < oligo.length()){
-                               success = 0;
+                               success = sdiffs+10;
                                break;
                        }
                        
@@ -807,7 +807,7 @@ bool TrimOligos::stripSpacer(Sequence& seq, QualityScores& qual){
                                if(qual.getName() != ""){
                                        qual.trimQScores(oligo.length(), -1);
                                }
-                               success = 1;
+                               success = 0;
                                break;
                        }
                }
@@ -904,19 +904,19 @@ bool TrimOligos::stripSpacer(Sequence& seq){
        try {
                
                string rawSequence = seq.getUnaligned();
-               bool success = 0;       //guilty until proven innocent
+               bool success = sdiffs+1;        //guilty until proven innocent
                
                for(int i=0;i<spacer.size();i++){
                        string oligo = spacer[i];
                        
                        if(rawSequence.length() < oligo.length()){
-                               success = 0;
+                               success = sdiffs+10;
                                break;
                        }
                        
                        if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
                                seq.setUnaligned(rawSequence.substr(oligo.length()));
-                               success = 1;
+                               success = 0;
                                break;
                        }
                }