fixes while testing 1.33.0

[mothur.git] / trimoligos.cpp

diff --git a/trimoligos.cpp b/trimoligos.cpp
index 504a8b59e35b2e99567e7085ccd964b43d8d8361..0f2a9cbb0e584ddfa393a53015b02b37ccfa3903 100644 (file)
--- a/trimoligos.cpp
+++ b/trimoligos.cpp
@@ -368,6 +368,8 @@ int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
                 temp = temp.substr(0,alnLength);
                 int numDiff = countDiffs(oligo, temp);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " aligned fragment =" + temp + ", barcode =" + oligo + ", numDiffs = " + toString(numDiff) + "\n"); }
+                
                 if(numDiff < minDiff){
                     minDiff = numDiff;
                     minCount = 1;
@@ -487,6 +489,8 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& gr
                 temp = temp.substr(0,alnLength);
                 int numDiff = countDiffs(oligo, temp);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                
                 if (alnLength == 0) { numDiff = bdiffs + 100; }
                 //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
                 
@@ -548,6 +552,9 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& gr
                     oligo = oligo.substr(0,alnLength);
                     temp = temp.substr(0,alnLength);
                     int numDiff = countDiffs(oligo, temp);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                    
                     if (alnLength == 0) { numDiff = bdiffs + 100; }
                     
                     //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
@@ -700,7 +707,7 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, Quality
                 int numDiff = countDiffs(oligo, temp);
                 
                 if (alnLength == 0) { numDiff = bdiffs + 100; }
-                //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+                if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
                 
                 if(numDiff < minDiff){
                     minDiff = numDiff;
@@ -762,6 +769,8 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, Quality
                     int numDiff = countDiffs(oligo, temp);
                     if (alnLength == 0) { numDiff = bdiffs + 100; }
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse " + reverseSeq.getName() + " aligned fragment=" + temp + ", barcode=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                    
                     //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
                     if(numDiff < minDiff){
                         minDiff = numDiff;
@@ -855,6 +864,8 @@ int TrimOligos::stripPairedBarcode(Sequence& seq, QualityScores& qual, int& grou
                 break;
             }
             
+            if (rawSeq.length() < (foligo.length() + roligo.length())) {  success = pdiffs + 10; break; }
+            
             if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
                 group = it->first;
                 string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
@@ -1078,6 +1089,8 @@ int TrimOligos::stripPairedPrimers(Sequence& seq, QualityScores& qual, int& grou
                 break;
             }
             
+            if (rawSeq.length() < (foligo.length() + roligo.length())) {  success = pdiffs + 10; break; }
+            
             if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
                 group = it->first;
                 if (!keepForward) {
@@ -1366,6 +1379,8 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, Quality
                 if (alnLength == 0) { numDiff = pdiffs + 100; }
                 //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                
                 if(numDiff < minDiff){
                     minDiff = numDiff;
                     minCount = 1;
@@ -1426,6 +1441,8 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, Quality
                     int numDiff = countDiffs(oligo, temp);
                     if (alnLength == 0) { numDiff = pdiffs + 100; }
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                    
                     //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
                     if(numDiff < minDiff){
                         minDiff = numDiff;
@@ -1575,6 +1592,8 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& gr
                 temp = temp.substr(0,alnLength);
                 int numDiff = countDiffs(oligo, temp);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: forward " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                
                 if (alnLength == 0) { numDiff = pdiffs + 100; }
                 //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
                 
@@ -1636,6 +1655,9 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& gr
                     oligo = oligo.substr(0,alnLength);
                     temp = temp.substr(0,alnLength);
                     int numDiff = countDiffs(oligo, temp);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse " + forwardSeq.getName() + " aligned fragment=" + temp + ", primer=" + oligo + ", numDiffs=" + toString(numDiff) + ".\n");  }
+                    
                     if (alnLength == 0) { numDiff = pdiffs + 100; }
                     
                     //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
@@ -1769,6 +1791,8 @@ int TrimOligos::stripBarcode(Sequence& seq, int& group){
                 
                 int numDiff = countDiffs(oligo, temp);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " aligned fragment =" + temp + ", barcode =" + oligo + ", numDiffs = " + toString(numDiff) + "\n"); }
+                
                 if(numDiff < minDiff){
                     minDiff = numDiff;
                     minCount = 1;