fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index aafa5794e206b936793cf6ffce6109f66eebaf86..4dd5b38d4f7ab3895d7fa305bdb57f2e9ab5a628 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -16,6 +16,7 @@ QualityScores::QualityScores(){
                m = MothurOut::getInstance();
                seqName = "";
                seqLength = -1;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "QualityScores", "QualityScores");
@@ -197,9 +198,12 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
                        }
                }
                
+               //every score passed
+               if (end == (seqLength-1)) { end = seqLength; }
+               
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);
-       
+               
                return 1;
        }
        catch(exception& e) {
@@ -237,9 +241,11 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
                
                if(end == -1){  end = seqLength;        }
                
+               
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);
                
+               
                return 1;
        }
        catch(exception& e) {
@@ -286,6 +292,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                
                if(end == -1){  end = seqLength;        }
                
+               
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);