changed get.sharedotu to get.sharedseqs

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 14973ccc3c65d05952783acaf3ba03431e842106..51fc0e7b3a93265eee63092adfe5ea75cdb87f6b 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -122,7 +122,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 
                        
                        
-                       if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
+                       if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
                        
 
                }
@@ -168,6 +168,8 @@ void ChimeraSeqsCommand::help(){
                mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n"); 
                mothurOut("\tchimeracheck: \n"); 
                mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n"); 
+               mothurOut("\tchimeraslayer: \n"); 
+               mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); 
                mothurOut("The chimera.seqs command should be in the following format: \n");
                mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
                mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c85326854b1253710f8f56e7bcacf37290cc1ed5..635cff032a645b7e69c168c7b461eaca71bb364d 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -114,7 +114,7 @@ CommandFactory::CommandFactory(){
        commands["system"]                              = "system";
        commands["align.check"]                 = "align.check";
        commands["get.sharedseqs"]              = "get.sharedseqs";
-       commands["get.listcount"]               = "get.listcount";
+       commands["get.otulist"]                 = "get.otulist";
        commands["quit"]                                = "quit"; 
        commands["hcluster"]                    = "hcluster"; 
        commands["classify.seqs"]               = "classify.seqs"; 
@@ -182,7 +182,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
                else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
                else if(commandName == "get.sharedseqs")                        {       command = new GetSharedOTUCommand(optionString);                }
-               else if(commandName == "get.listcount")                 {       command = new GetListCountCommand(optionString);                }
+               else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                }
                else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
                else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                   }