added mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51fa43b39f87f06a3054808acb4937e05ae2337f..ec809730a036245f34dfc2bc0331b108c5d10b38 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
         }
         CountTable ct;
         if (countfile != "")  {  
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (countfile == outCountFile){
                 //prepare filenames and open files
                 map<string, string> mvariables;
@@ -286,7 +286,7 @@ int DeconvoluteCommand::execute() {
                        
                        m->gobble(in);
                        
-                       if(count % 1000 == 0)   { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();       }
+                       if(count % 1000 == 0)   { m->mothurOutJustToScreen(toString(count) + "\t" + toString(sequenceStrings.size()) + "\n");   }
                }
                
                if(count % 1000 != 0)   { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();       }