done testing 1.14.0

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 4a328a3bca837ad2b90ef16b0722aa5bdad21d30..a677e4c9b9e115fd647b60cf45983a0c50b06fbf 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1112,7 +1112,6 @@
                        };
                        buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.0";
-                       developmentRegion = English;
                        hasScannedForEncodings = 1;
                        knownRegions = (
                                English,

diff --git a/makefile b/makefile
index 4e0571804d1d88598867f89f5f55ae09167121e0..3d0e18de0e40d3b035f101c857c6def36e8cbdfd 100644 (file)
--- a/makefile
+++ b/makefile
@@ -28,9 +28,9 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
         CXXFLAGS += -DBIT_VERSION
 endif
 
-MOTHUR_FILES = "\"../Release\""
+MOTHUR_FILES = "\"../release\""
 
-RELEASE_DATE = "\"10/22/2010\""
+RELEASE_DATE = "\"10/26/2010\""
 VERSION = "\"1.14.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}

diff --git a/mothur b/mothur
index 1255e3acd4e73f2c99d45e4b5787783daf36800d..f752264a5db4857142f01ff205b52525364b3da8 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index ae2663df8e63b117995b3442227f72343e194bbb..a174cce11a3b4c928c3b08a817d534ad149822bb 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -358,6 +358,8 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt
                                
                if (name == "system") { return false; }
                
+               if (name == "system") { return false; }
+               
                //get shell of the command so we can check to make sure its valid without running it
                Command* command = cFactory->getCommand(name);
                        

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index c0e04d569604ee0aa67c29ceefbda06275a2df9d..f1804ed8b826d00b4993a708804733335bb1b194 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -404,7 +404,7 @@ int RemoveSeqsCommand::readName(){
                while(!in.eof()){
                        if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 
-                       in >> firstCol;                         
+                       in >> firstCol;         m->gobble(in);          
                        in >> secondCol;                        
 
                        vector<string> parsedNames;

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 8a7a108eb322978377a9d09ffb880a2745c54caf..30dda1f68518bf395ae0cbb892cf71a3a7ded4d5 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -1007,6 +1007,9 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
                                        delete buf3;
                                }
                        }
+                       
+                       //report progress
+                       if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
                }
                                
                return 1;