X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=trimseqscommand.cpp;h=b430624838594e4185233f7e946733a94469303b;hb=bbdb72971ea4cd171abe34985af89f97bc2a31d3;hp=5a0124934bfaeb682914d62aff34a25f04b4a3ab;hpb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5a01249..b430624 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -322,11 +322,20 @@ int TrimSeqsCommand::execute(){
 				openInputFile(fastaFile, inFASTA);
 				getNumSeqs(inFASTA, numSeqs);
 				inFASTA.close();
-				qFile.close();
+				
 				lines.push_back(new linePair(0, numSeqs));
 				
 				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
 				
+				for (int j = 0; j < fastaFileNames.size(); j++) {
+					rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
+				}
+				if(qFileName != ""){
+					for (int j = 0; j < qualFileNames.size(); j++) {
+						rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
+					}
+				}
+									
 				if (m->control_pressed) {  return 0; }
 		#endif
 						
@@ -479,7 +488,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			Sequence currSeq(inFASTA);
 			QualityScores currQual;
 			if(qFileName != ""){
-				currQual = QualityScores(qFile);
+				currQual = QualityScores(qFile, currSeq.getNumBases());
 			}
 			
 			string origSeq = currSeq.getUnaligned();
@@ -1220,9 +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;