Merge branch 'master' into v.1.38.0

mothur · feff7c55f6042ed8efd390568ad981648d1a55c2 · mothur-westcott committed Jun 30, 2016 · Jun 30, 2016 · feff7c5
2 parents 50c9d93 + 12cb0f7
commit feff7c55f6042ed8efd390568ad981648d1a55c2
diff --git a/Makefile b/Makefile
@@ -13,9 +13,10 @@ OPTIMIZE ?= yes
 USEREADLINE ?= yes
 USEBOOST ?= yes
 BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"4/05/2016\""
-VERSION = "\"1.37.0\""
+RELEASE_DATE = "\"6/20/2016\""
+VERSION = "\"1.37.6\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION
@@ -44,7 +45,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
 endif
 
 
-#The boost libraries allow you to read gz files.
+#User specified boost library
 ifeq  ($(strip $(USEBOOST)),yes)
 
     LDFLAGS += -L ${BOOST_LIBRARY_DIR}
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
@@ -3335,6 +3335,11 @@
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_PREPROCESSOR_DEFINITIONS = (
+					"VERSION=\"\\\"1.37.1\\\"\"",
+					"RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_FUNCTION = YES;
@@ -3344,6 +3349,7 @@
 					/usr/local/lib/,
 					/usr/local/include/,
 				);
+				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
 				PRODUCT_NAME = mothur;
 				SDKROOT = macosx;
@@ -3364,6 +3370,11 @@
 				DSTROOT = TARGET_BUILD_DIR;
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_PREPROCESSOR_DEFINITIONS = (
+					"VERSION=\"\\\"1.37.1\\\"\"",
+					"RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_VALUE = YES;
@@ -3438,8 +3449,9 @@
 				GCC_MODEL_TUNING = "";
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.36.0\\\"\"",
-					"RELEASE_DATE=\"\\\"07/23/2015\\\"\"",
+					"VERSION=\"\\\"1.37.6\\\"\"",
+					"RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
+					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_VERSION = "";
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
@@ -3537,8 +3549,8 @@
 				ENABLE_STRICT_OBJC_MSGSEND = YES;
 				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.37.0\\\"\"",
-					"RELEASE_DATE=\"\\\"04/05/2015\\\"\"",
+					"VERSION=\"\\\"1.37.6\\\"\"",
+					"RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
 				);
 				GCC_WARN_64_TO_32_BIT_CONVERSION = NO;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES_ERROR;
diff --git a/makefile-internal b/makefile-internal
@@ -45,7 +45,7 @@ ifeq  ($(strip $(USEBOOST)),yes)
     LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a
 
     #if mac
-    LIBS += ${BOOST_LIBRARY_DIR}/zlib.a
+    LIBS += -lz
 
     #if linux or windows
     #LIBS += ${BOOST_LIBRARY_DIR}/libz.a
diff --git a/source/commands/chimerauchimecommand.cpp b/source/commands/chimerauchimecommand.cpp
@@ -675,7 +675,7 @@ int ChimeraUchimeCommand::execute(){
 				if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
 				if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
 				
-				m->printVsearchFile(nameMapCount, newFasta);
+                m->printVsearchFile(nameMapCount, newFasta, "ab");
 				fastaFileNames[s] = newFasta;
 			}
 			
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
diff --git a/source/commands/makecontigscommand.h b/source/commands/makecontigscommand.h
diff --git a/source/commands/pcrseqscommand.cpp b/source/commands/pcrseqscommand.cpp
@@ -878,7 +878,7 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
                 if (totalDiffs > pdiffs) { trashCode += "t"; goodSeq = false; }
                 
                 //trimming removed all bases
-               // if (currSeq.getUnaligned() == "") { goodSeq = false; }
+                if (currSeq.getUnaligned() == "") { goodSeq = false; }
                 
 				if(goodSeq == 1)    {
                     currSeq.printSequence(goodFile);
diff --git a/source/mothurout.cpp b/source/mothurout.cpp
@@ -3431,7 +3431,7 @@ bool MothurOut::mothurConvert(string item, intDist& num){
 string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
     try{
         string newTax, taxon;
-        int level = 0;
+        int level = 1;
         
         vector<string> taxons; splitAtChar(tax, taxons, ';'); taxons.pop_back();
         vector<int> confidences;
@@ -3447,7 +3447,7 @@ string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
             if (thisTax == "unclassified;"){ index--; break; }
             else{ newTax += taxons[i] + ";";  }
         }
-        level = index+1;
+        level = index+2;
         
         string thisTax = taxons[index]+";";
         
@@ -4873,7 +4873,7 @@ int MothurOut::min(int A, int B){
     }
 }
 //**********************************************************************************************************************
-int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string filename){
+int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string filename, string tag){
     try {
         
         sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
@@ -4884,7 +4884,7 @@ int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string fi
         //print new file in order of
         for (int i = 0; i < nameMapCount.size(); i++) {
             if (control_pressed) {break;}
-            out << ">" << nameMapCount[i].name  << "/size=" << nameMapCount[i].numIdentical << "/" << endl << nameMapCount[i].seq << endl;
+            out << ">" << nameMapCount[i].name  << "/" + tag + "=" << nameMapCount[i].numIdentical << "/" << endl << nameMapCount[i].seq << endl;
         }
         out.close();
         
diff --git a/source/mothurout.h b/source/mothurout.h
@@ -140,7 +140,7 @@ class MothurOut {
 		int readNames(string, map<string, vector<string> >&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
-        int printVsearchFile(vector<seqPriorityNode>&, string); //sorts and prints by abundance adding /ab=xxx/
+        int printVsearchFile(vector<seqPriorityNode>&, string, string); //sorts and prints by abundance adding /ab=xxx/
         bool mothurConvert(char, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
         bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
diff --git a/source/optionparser.cpp b/source/optionparser.cpp
@@ -23,13 +23,17 @@ OptionParser::OptionParser(string option) {
 				m->splitAtEquals(key, value);
 				if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 				if (key == "template") { key = "reference"; }
+				key = m->splitWhiteSpace(key).front();
+			    value = m->splitWhiteSpace(value).front();
 				parameters[key] = value;
 			}
 			
 			//in case there is no comma and to get last parameter after comma
 			m->splitAtEquals(key, option);
 			if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 			if (key == "template") { key = "reference"; }
+            key = m->splitWhiteSpace(key).front();
+			option = m->splitWhiteSpace(option).front();
 			parameters[key] = option;
 		}
 	}
@@ -52,13 +56,17 @@ OptionParser::OptionParser(string option, map<string, string>& copy) {
 				m->splitAtEquals(key, value);
 				if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 				if (key == "template") { key = "reference"; }
+				key = m->splitWhiteSpace(key).front();
+			    value = m->splitWhiteSpace(value).front();
 				parameters[key] = value;
 			}
 			
 			//in case there is no comma and to get last parameter after comma
 			m->splitAtEquals(key, option);
 			if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 			if (key == "template") { key = "reference"; }
+			key = m->splitWhiteSpace(key).front();
+			option = m->splitWhiteSpace(option).front();
 			parameters[key] = option;
 		}
         
diff --git a/source/read/splitmatrix.cpp b/source/read/splitmatrix.cpp
@@ -686,6 +686,7 @@ int SplitMatrix::splitNamesVsearch(map<string, int>& seqGroup, int numGroups, ve
             }
         }
         bigNameFile.close();
+
         
         for(int i=0;i<numGroups;i++){
             string tempNameFile = inputFile + "." + toString(i) + ".temp";
diff --git a/source/vsearchfileparser.cpp b/source/vsearchfileparser.cpp
@@ -111,7 +111,7 @@ string VsearchFileParser::createVsearchFasta(string inputFile){
         }
         in.close();
         
-        m->printVsearchFile(seqs, vsearchFasta);
+        m->printVsearchFile(seqs, vsearchFasta, "size");
         
         return vsearchFasta;
     }