X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimseqscommand.h;h=53f04d37965d55c189447c7cbd1c702ac93dc5ac;hp=4d0a6112cb6e288600ae944e9340563f5973da47;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hpb=8d341208b0cd0c7a4ff8b77c6b164e06f2f39610

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4d0a611..53f04d3 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -261,7 +261,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 		
         TrimOligos* trimOligos = NULL;
         int numBarcodes = pDataArray->barcodes.size();
-        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); }
+        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); pDataArray->numFPrimers = pDataArray->pairedPrimers.size(); }
         else                {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);  }
         
         TrimOligos* rtrimOligos = NULL;
@@ -283,7 +283,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 		for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
 			           
 			if (pDataArray->m->control_pressed) {
-                delete trimOligos;
+                delete trimOligos; if (pDataArray->reorient) { delete rtrimOligos; }
 				inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
 				if ((pDataArray->createGroup) && (pDataArray->countfile == "")) {	 outGroupsFile.close();   }
                 if(pDataArray->qFileName != "")	{	qFile.close();	scrapQualFile.close(); trimQualFile.close();	}
@@ -299,11 +299,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 			int currentSeqsDiffs = 0;
             
 			Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);
+            Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
 			
-			QualityScores currQual;
+			QualityScores currQual; QualityScores savedQual;
 			if(pDataArray->qFileName != ""){
 				currQual = QualityScores(qFile);  pDataArray->m->gobble(qFile);
+                savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
 			}
+              
 			
 			string origSeq = currSeq.getUnaligned();
 			if (origSeq != "") {
@@ -353,13 +356,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                     int thisPrimerIndex = 0;
                     
                     if(numBarcodes != 0){
-                        thisSuccess = rtrimOligos->stripBarcode(currSeq, currQual, thisBarcodeIndex);
+                        thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
                         if(thisSuccess > pDataArray->bdiffs)		{	thisTrashCode += 'b';	}
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                     
                     if(pDataArray->numFPrimers != 0){
-                        thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, pDataArray->keepforward);
+                        thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, pDataArray->keepforward);
                         if(thisSuccess > pDataArray->pdiffs)		{	thisTrashCode += 'f';	}
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
@@ -372,7 +375,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
-                    }
+                        savedSeq.reverseComplement();
+                        currSeq.setAligned(savedSeq.getAligned());
+                        if(pDataArray->qFileName != ""){
+                            savedQual.flipQScores();
+                            currQual.setScores(savedQual.getScores());
+                        }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }
 
                 
@@ -567,12 +576,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 			}
 			
 			//report progress
-			if((i) % 1000 == 0){	pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();		}
+			if((pDataArray->count) % 1000 == 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
 			
 		}
 		//report progress
 		if((pDataArray->count) % 1000 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
 		
+        if (pDataArray->reorient) { delete rtrimOligos; }
 		delete trimOligos;
 		inFASTA.close();
 		trimFASTAFile.close();