Enhances error checks make.contigs

Mothur.xcodeproj/project.pbxproj

@@ -3370,8 +3370,8 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_CXX0X_EXTENSIONS = YES;
 				"CLANG_WARN_CXX0X_EXTENSIONS[arch=*]" = NO;
 				CLANG_WARN_UNREACHABLE_CODE = YES;
@@ -3393,10 +3393,7 @@
 				GCC_WARN_UNUSED_FUNCTION = YES;
 				"INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
 				LIBRARY_SEARCH_PATHS = "";
-				"LIBRARY_SEARCH_PATHS[arch=*]" = (
-					/usr/local/lib/,
-					/usr/local/include/,
-				);
+				"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
 				PRODUCT_NAME = mothur;
@@ -3409,8 +3406,8 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_CXX0X_EXTENSIONS = YES;
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
@@ -3426,10 +3423,7 @@
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_VALUE = YES;
-				LIBRARY_SEARCH_PATHS = (
-					/usr/local/include/,
-					/usr/local/lib/,
-				);
+				LIBRARY_SEARCH_PATHS = /usr/local/lib/;
 				"LIBRARY_SEARCH_PATHS[arch=*]" = "";
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
@@ -3443,8 +3437,8 @@
 		1DEB928A08733DD80010E9CD /* Debug */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEPLOYMENT_LOCATION = NO;
 				ENABLE_TESTABILITY = YES;
@@ -3465,8 +3459,11 @@
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_FUNCTION = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
-				HEADER_SEARCH_PATHS = /usr/local/include/;
-				"HEADER_SEARCH_PATHS[arch=*]" = "";
+				HEADER_SEARCH_PATHS = "";
+				"HEADER_SEARCH_PATHS[arch=*]" = (
+					"$(inherited)",
+					/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include,
+				);
 				INSTALL_PATH = TARGET_BUILD_DIR;
 				LIBRARY_SEARCH_PATHS = "";
 				"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
@@ -3475,12 +3472,10 @@
 				ONLY_ACTIVE_ARCH = YES;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DBIT_VERSION",
-					"-DUSE_BOOST",
 					"-DUNIT_TEST",
-					"-stdlib=libstdc++",
-					"-std=c++11",
 					"-DUSE_READLINE",
 					"$(OTHER_CFLAGS)",
+					"-DUSE_BOOST",
 				);
 				OTHER_LDFLAGS = (
 					"-lreadline",
@@ -3496,8 +3491,8 @@
 		1DEB928B08733DD80010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEPLOYMENT_LOCATION = NO;
 				GCC_C_LANGUAGE_STANDARD = c11;
@@ -3530,12 +3525,10 @@
 				MACOSX_DEPLOYMENT_TARGET = 10.12;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DUSE_READLINE",
-					"-DUSE_BOOST",
 					"-DUNIT_TEST",
-					"-std=c++11",
-					"-stdlib=libstdc++",
 					"-DBIT_VERSION",
 					"$(OTHER_CFLAGS)",
+					"-DUSE_BOOST",
 				);
 				OTHER_LDFLAGS = (
 					"-lreadline",

source/commands/makecontigscommand.cpp

@@ -2098,6 +2098,7 @@ unsigned long long MakeContigsCommand::driver(vector<string> inputFiles, vector<
                         outScrapQual << ">" << fSeq.getName() << " | " << trashCode << '\t' << commentString << endl;
                         for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << " "; }  outScrapQual << endl;
                     }
+                    
                 }
             }
             num++;
@@ -2302,17 +2303,18 @@ vector<int> MakeContigsCommand::assembleFragments(vector< vector<double> >&qual_
             for (int i = overlapEnd; i < length; i++) {  contig += seq1[i];  if (hasQuality) { if (((seq1[i] != '-') && (seq1[i] != '.'))) { contigScores.push_back(scores1[ABaseMap[i]]); } }
             }
         }
-        //cout << contig << endl;
+        //cout << "contig = " << contig << endl;
         
         if (trimOverlap) {
             contig = contig.substr(overlapStart, oend-oStart);
-            if (contig.length() == 0) { trashCode += "l"; }
             if (hasQuality) {
                 vector<int> newContigScores;
                 for (int i = overlapStart; i < oend; i++)  { newContigScores.push_back(contigScores[i]);  }
                 contigScores = newContigScores;
             }
         }
+        
+        if (contig == "") { trashCode += "l"; contig = "NNNN"; contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); }
 
         return contigScores;
     }

source/commands/makecontigscommand.h

@@ -1939,6 +1939,8 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
                         }
                     }
                     
+                    if (contig == "") { trashCode += "l"; contig = "NNNN"; contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); }
+                    
                     if(trashCode.length() == 0){
                         bool ignore = false;
                         
@@ -3281,6 +3283,8 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
                     }
                 }
                 
+                if (contig == "") { trashCode += "l"; contig = "NNNN"; contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); contigScores.push_back(0); }
+                
                 if(trashCode.length() == 0){
                     bool ignore = false;