X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=580fc22c978e0105b464e214593599fe15970f1d;hb=f07bf12e0d04340698aff7a36d2fee7c959ffe59;hp=705ac25f5a5e727424a2567a0d358b4c1dc951e5;hpb=8ef6687c1f586285d01c000cc5e359bf9c07c717;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 705ac25..580fc22 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -163,7 +163,7 @@ void TrimSeqsCommand::help(){
 		m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 		m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 		m->mothurOut("The fasta parameter is required.\n");
-		m->mothurOut("The flip parameter .... The default is 0.\n");
+		m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 		m->mothurOut("The oligos parameter .... The default is "".\n");
 		m->mothurOut("The maxambig parameter .... The default is -1.\n");
 		m->mothurOut("The maxhomop parameter .... The default is 0.\n");
@@ -224,8 +224,9 @@ int TrimSeqsCommand::execute(){
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
 					ifstream inFASTA;
+					int numSeqs;
 					openInputFile(fastaFile, inFASTA);
-					int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					getNumSeqs(inFASTA, numSeqs);
 					inFASTA.close();
 					
 					lines.push_back(new linePair(0, numSeqs));
@@ -266,8 +267,9 @@ int TrimSeqsCommand::execute(){
 				if (m->control_pressed) {  return 0; }
 		#else
 				ifstream inFASTA;
+				int numSeqs;
 				openInputFile(fastaFile, inFASTA);
-				int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numSeqs));
@@ -650,7 +652,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 						maxLength = it->first.length();
 					}
 				}
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));  
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));  
 
 			}else{ alignment = NULL; } 
 			
@@ -684,6 +686,9 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 				
 				int newStart=0;
 				int numDiff = countDiffs(oligo, temp);
+				
+//				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
+				
 				if(numDiff < minDiff){
 					minDiff = numDiff;
 					minCount = 1;
@@ -764,7 +769,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
 						maxLength = forPrimer[i].length();
 					}
 				}
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));  
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));  
 
 			}else{ alignment = NULL; }