paralellized make.table / count.seqs command. added getCopy function to groupMap...

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 5fa71bef6b3474cc516491044c41729a318d449f..f2ca9db29d7a94ce0d22606d4ad114e11001fd4f 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -696,10 +696,10 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
 #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");       }
                
         badFile.close();
                goodFile.close();
@@ -804,7 +804,7 @@ bool PcrSeqsCommand::readOligos(){
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                         char c = inOligos.get(); 
-                        if (c == 10 || c == 13){       break;  } 
+                        if (c == 10 || c == 13 || c == -1){    break;  }
                         else if (c == 32 || c == 9){;} //space or tab
                                        } 
                                        primers[oligo] = primerCount; primerCount++;
@@ -1088,7 +1088,7 @@ int PcrSeqsCommand::readCount(set<string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }