X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=2dc07794be5abb2f239e4b228c3aacbf51c51b6e;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=9fc3abb8422341e755a1e54da38453002cf01dce;hpb=15cde0905641f8adddc1cc704f8c064f760e7461;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 9fc3abb..2dc0779 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -11,6 +11,7 @@
 #include "needlemanoverlap.hpp"
 
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getValidParameters(){	
 	try {
 		string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile", 
@@ -25,7 +26,9 @@ vector<string> TrimSeqsCommand::getValidParameters(){
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
+
 TrimSeqsCommand::TrimSeqsCommand(){	
 	try {
 		abort = true;
@@ -40,7 +43,9 @@ TrimSeqsCommand::TrimSeqsCommand(){
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getRequiredParameters(){	
 	try {
 		string Array[] =  {"fasta"};
@@ -52,7 +57,9 @@ vector<string> TrimSeqsCommand::getRequiredParameters(){
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getRequiredFiles(){	
 	try {
 		vector<string> myArray;
@@ -63,6 +70,7 @@ vector<string> TrimSeqsCommand::getRequiredFiles(){
 		exit(1);
 	}
 }
+
 //***************************************************************************************************************
 
 TrimSeqsCommand::TrimSeqsCommand(string option)  {
@@ -254,6 +262,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
 
 void TrimSeqsCommand::help(){
@@ -446,7 +455,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 	try {
 		
 		ofstream outFASTA;
-		int able = m->openOutputFile(trimFile, outFASTA);
+		m->openOutputFile(trimFile, outFASTA);
 		
 		ofstream scrapFASTA;
 		m->openOutputFile(scrapFile, scrapFASTA);
@@ -547,16 +556,16 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 				
 				if(qFileName != ""){
+					int origLength = currSeq.getNumBases();
 					
 					if(qThreshold != 0)			{	success = currQual.stripQualThreshold(currSeq, qThreshold);			}
 					else if(qAverage != 0)		{	success = currQual.cullQualAverage(currSeq, qAverage);				}
 					else if(qRollAverage != 0)	{	success = currQual.stripQualRollingAverage(currSeq, qRollAverage);	}
 					else if(qWindowAverage != 0){	success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);	}
 					else						{	success = 1;				}
-
-//					if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) { 
-//						success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
-//					}
+					
+					//you don't want to trim, if it fails above then scrap it
+					if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
 					
 					if(!success)				{	trashCode += 'q';	}
 				}				
@@ -874,6 +883,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned
 		exit(1);
 	}
 }
+
 //***************************************************************************************************************
 
 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
@@ -1085,7 +1095,6 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group
 				oligo = oligo.substr(0,alnLength);
 				temp = temp.substr(0,alnLength);
 				
-				int newStart=0;
 				int numDiff = countDiffs(oligo, temp);
 				
 //				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
@@ -1210,7 +1219,6 @@ int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group
 				oligo = oligo.substr(0,alnLength);
 				temp = temp.substr(0,alnLength);
 				
-				int newStart=0;
 				int numDiff = countDiffs(oligo, temp);
 				
 //				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
@@ -1433,6 +1441,7 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 	}
 
 }
+
 //***************************************************************************************************************
 
 int TrimSeqsCommand::countDiffs(string oligo, string seq){