working on chimera.uchime change for dereplicate=t bug. added shared file to get...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4d0a6112cb6e288600ae944e9340563f5973da47..882f716357515b008c06889f3f1559a4e4525cd5 100644 (file)
--- 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();    }
@@ -372,6 +372,10 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
+                        currSeq.reverseComplement();
+                        if(pDataArray->qFileName != ""){
+                            currQual.flipQScores();
+                        }
                     }
                 }
 
@@ -567,12 +571,13 @@ 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();