fixed bug in make.biom that occurred if some taxonomies had confidence scores and...

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 6dbe6261b778dffbaea00c3940416d93f98ea049..ae1df1e962214992fc05f97c4fde02420ea9d735 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -367,7 +367,7 @@
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
-               8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
@@ -1150,7 +1150,7 @@
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* Mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
@@ -1809,7 +1809,7 @@
                        name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
@@ -2183,9 +2183,9 @@
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
                                SDKROOT = macosx10.6;
-                               SYMROOT = "";
+                               SKIP_INSTALL = NO;
                        };
                        name = Debug;
                };
@@ -2197,8 +2197,8 @@
                                DEPLOYMENT_LOCATION = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               PRODUCT_NAME = Mothur;
-                               SYMROOT = "";
+                               PRODUCT_NAME = mothur;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
@@ -2222,7 +2222,7 @@
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                HEADER_SEARCH_PATHS = "";
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
@@ -2235,6 +2235,7 @@
                                        "-lreadline",
                                );
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
@@ -2260,7 +2261,7 @@
                                GCC_WARN_UNUSED_PARAMETER = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
@@ -2272,6 +2273,7 @@
                                        "-lreadline",
                                );
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index acd0500963d096acfb5d1ea453cc9186feafe783..03e7baf2b9888fc7f52cbe6076ea8fdfa472b584 100644 (file)
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -165,7 +165,7 @@ MakeBiomCommand::MakeBiomCommand(string option) {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                       
+
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["biom"] = tempOutNames;
@@ -612,7 +612,7 @@ vector<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
                         scores.push_back(confidenceScore);
                                        }else{ scores.push_back("null"); }
                                }
-                       }
+                       }else{ scores.push_back("null"); }
                        
             //strip "" if they are there
             pos = taxon.find("\"");

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 803b6cb7955af18d441d6c160e5aafb797c3a057..508e2a90610d1b3705972a976580d90937358427 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -136,7 +136,7 @@ ShhherCommand::ShhherCommand(string option) {
                        flowFileName = validParameter.validFile(parameters, "flow", true);
                        flowFilesFileName = validParameter.validFile(parameters, "file", true);
                        if (flowFileName == "not found" && flowFilesFileName == "not found") {
-                               m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
+                               m->mothurOut("values for either flow or file must be provided for the shhh.flows command.");
                                m->mothurOutEndLine();
                                abort = true; 
                        }