X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.h;h=b61ebda3fc505db3c6805706cafb2e337138474d;hb=1f0e54b53b714781f3f2fee7d01177fade98a625;hp=65b365840573cde71902c153a499c07530e0a79a;hpb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;p=mothur.git

diff --git a/makecontigscommand.h b/makecontigscommand.h
index 65b3658..b61ebda 100644
--- a/makecontigscommand.h
+++ b/makecontigscommand.h
@@ -60,7 +60,7 @@ public:
     
 private:
     bool abort, allFiles, createGroup;
-    string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file;
+    string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file, format;
 	float match, misMatch, gapOpen, gapExtend;
 	int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
     vector<string> outputNames;
@@ -70,11 +70,13 @@ private:
     vector<string>  linker;
     vector<string>  spacer;
 	vector<string> primerNameVector;	
-	vector<string> barcodeNameVector;	
+	vector<string> barcodeNameVector;
+	vector<char> convertTable;
     
 	map<string, int> groupCounts; 
     map<string, string> groupMap;
     
+    vector<int> convertQual(string);
     fastqRead readFastq(ifstream&, bool&);
     vector< vector< vector<string> > > preProcessData(unsigned long int&);
     vector< vector<string> > readFileNames(string);
@@ -107,7 +109,7 @@ struct contigsData {
 	MothurOut* m;
 	float match, misMatch, gapOpen, gapExtend;
 	int count, threshold, threadID, pdiffs, bdiffs, tdiffs;
-    bool allFiles, createGroup;
+    bool allFiles, createGroup, done;
     map<string, int> groupCounts; 
     map<string, string> groupMap;
     vector<string> primerNameVector;	
@@ -143,6 +145,7 @@ struct contigsData {
         allFiles = all;
         createGroup = cg;
 		threadID = tid;
+        done=false;
 	}
 };
 
@@ -159,7 +162,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
         if(pDataArray->align == "gotoh")			{	alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase);			}
 		else if(pDataArray->align == "needleman")	{	alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase);				}
         
-        int num = 0;
+        pDataArray->count = 0;
         string thisffastafile = pDataArray->files[0];
         string thisfqualfile = pDataArray->files[1];
         string thisrfastafile = pDataArray->files[2];
@@ -335,6 +338,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
             }
 
             if(trashCode.length() == 0){
+                bool ignore = false;
                 if (pDataArray->createGroup) {
                     if(pDataArray->barcodes.size() != 0){
                         string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
@@ -350,16 +354,18 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
                         
                         if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
                         
-                        pDataArray->groupMap[fSeq.getName()] = thisGroup; 
-                        
-                        map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
-                        if (it == pDataArray->groupCounts.end()) {	pDataArray->groupCounts[thisGroup] = 1; }
-                        else { pDataArray->groupCounts[it->first] ++; }
+                        int pos = thisGroup.find("ignore");
+                        if (pos == string::npos) {
+                            pDataArray->groupMap[fSeq.getName()] = thisGroup; 
                         
+                            map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
+                            if (it == pDataArray->groupCounts.end()) {	pDataArray->groupCounts[thisGroup] = 1; }
+                            else { pDataArray->groupCounts[it->first] ++; }
+                        }else { ignore = true; }
                     }
                 }
                 
-                if(pDataArray->allFiles){
+                if(pDataArray->allFiles && !ignore){
                     ofstream output;
                     pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
                     output << ">" << fSeq.getName() << endl << contig << endl;
@@ -391,14 +397,14 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
                     outScrapQual << endl;
                 }
             }
-            num++;
+            pDataArray->count++;
             
 			//report progress
-			if((num) % 1000 == 0){	pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine();		}
+			if((pDataArray->count) % 1000 == 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
 		}
         
 		//report progress
-		if((num) % 1000 != 0){	pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine();		}
+		if((pDataArray->count) % 1000 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
         
         inFFasta.close();
         inRFasta.close();
@@ -413,6 +419,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
         }
         delete alignment;
         
+        pDataArray->done = true;
         if (pDataArray->m->control_pressed) {  pDataArray->m->mothurRemove(pDataArray->outputFasta);  pDataArray->m->mothurRemove(pDataArray->outputMisMatches);  pDataArray->m->mothurRemove(pDataArray->outputScrapFasta);  if (thisfqualfile != "") { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); } }
         
         return 0;