pat's slight modifications to trim.seqs

diff --git a/qualityscores.cpp b/qualityscores.cpp
index dd5d6de8da69a000882eadd86f8d2c50f853454f..29c81e295c883bc42d48830b59243f8961a273fb 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -220,8 +220,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                int seqLength = sequence.getNumBases();
                
                if(seqName != sequence.getName()){
-                       m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-                       m->mothurOutEndLine();  
+                       m->mothurOut("sequence name mismatch between fasta: " + sequence.getName() + " and qual file: " + seqName);
+                       m->mothurOutEndLine();
                }
                
                int end = windowSize;
@@ -237,7 +237,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                        double windowAverage = windowSum / (double)(end-start);
                        
                        if(windowAverage < qThreshold){
-                               end = start;
+                               end = end - stepSize;
                                break;
                        }
                        start += stepSize;

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a3abd597f0c3bdb9319849e675f722979d0c053f..b430624838594e4185233f7e946733a94469303b 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1229,9 +1229,9 @@ int TrimSeqsCommand::countDiffs(string oligo, string seq){
                                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++;   }                       
-                               
+                               else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }       
                        }
+                       
                }
                
                return countDiffs;