Fixing bugs for Windows compile

mothur · 933adb1f63b7a3b3490782cf9bfd955afce9e640 · mothur-westcott committed Dec 8, 2016 · Dec 8, 2016 · 933adb1
1 parent 7ee85e3
commit 933adb1f63b7a3b3490782cf9bfd955afce9e640
Unified Split

Showing with 13 additions and 11 deletions.

+4 −3 source/commands/chimeraperseuscommand.h

+4 −3 source/commands/chimerauchimecommand.h

+1 −1 source/commands/sffinfocommand.cpp

+2 −1 source/commands/shhhseqscommand.h

+2 −3 source/vsearchfileparser.cpp
diff --git a/source/commands/chimeraperseuscommand.h b/source/commands/chimeraperseuscommand.h
@@ -122,14 +122,15 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
 		//parse fasta and name file by group
 		SequenceParser* parser;
         SequenceCountParser* cparser;
+        vector<string> temp;
 		if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
             ct->readTable(pDataArray->namefile, true, false);
-            cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+            cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
             delete ct;
         }else {
-            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);	}
-            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);						}
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);	}
+            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp);						}
         }
     
 		int totalSeqs = 0;
diff --git a/source/commands/chimerauchimecommand.h b/source/commands/chimerauchimecommand.h
@@ -165,14 +165,15 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 		//parse fasta and name file by group
 		SequenceParser* parser;
         SequenceCountParser* cparser;
+        vector<string> temp;
 		if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
             ct->readTable(pDataArray->namefile, true, false);
-            cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+            cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
             delete ct;
         }else {
-            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);	}
-            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);						}
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);	}
+            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp);						}
         }
 		
 		int totalSeqs = 0;
diff --git a/source/commands/sffinfocommand.cpp b/source/commands/sffinfocommand.cpp
@@ -1383,7 +1383,7 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
         int currentSeqsDiffs = 0;
         
         string seq = read.bases;
-        
+        cout << header.clipQualLeft << endl;
         if (trim) {
             if(header.clipQualRight < header.clipQualLeft){
                 if (header.clipQualRight == 0) { //don't trim right
diff --git a/source/commands/shhhseqscommand.h b/source/commands/shhhseqscommand.h
@@ -103,7 +103,8 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
 	try {
 		
 		//parse fasta and name file by group
-		SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);
+        vector<string> temp;
+        SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);
 						
 		//precluster each group
 		for (int k = pDataArray->start; k < pDataArray->end; k++) {
diff --git a/source/vsearchfileparser.cpp b/source/vsearchfileparser.cpp
@@ -62,7 +62,7 @@ string VsearchFileParser::getVsearchFile() {
         if (fastafile == "") { m->mothurOut("[ERROR]: no fasta file given, cannot continue.\n"); m->control_pressed = true;  }
         
         //Run unique.seqs on the data if a name or count file is not given
-        if ((namefile == "") && (countfile == ""))  {  countfile = getNamesFile(fastafile);     }
+        if ((namefile == "") && (countfile == ""))  {  getNamesFile(fastafile);                }
         else if (namefile != "")                    {  counts = m->readNames(namefile);        }
         
         if (countfile != "") { CountTable countTable; countTable.readTable(countfile, false, false);  counts = countTable.getNameMap(); }
@@ -124,7 +124,6 @@ string VsearchFileParser::createVsearchFasta(string inputFile){
 
 string VsearchFileParser::getNamesFile(string& inputFile){
     try {
-        string nameFile = "";
         
         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
         
@@ -146,7 +145,7 @@ string VsearchFileParser::getNamesFile(string& inputFile){
         countfile = filenames["count"][0];
         fastafile = filenames["fasta"][0];
         
-        return nameFile;
+        return countfile;
     }
     catch(exception& e) {
         m->errorOut(e, "VsearchFileParser", "getNamesFile");