From: pschloss <pschloss>
Date: Wed, 28 Jul 2010 14:55:58 +0000 (+0000)
Subject: pat's slight modifications to trim.seqs
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=bbdb72971ea4cd171abe34985af89f97bc2a31d3

pat's slight modifications to trim.seqs
---

diff --git a/qualityscores.cpp b/qualityscores.cpp
index dd5d6de..29c81e2 100644
--- 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 a3abd59..b430624 100644
--- 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;