working on chimeraslayer and found bug in shared command.

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 925de63c17bf44011e9bb29e1e4b9a7a980fd3ff..f368869449242ff52fc4c6bce4057a0a17013798 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -26,7 +26,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "printall" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -78,6 +78,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
                        correction = isTrue(temp);
                        
+                       temp = validParameter.validFile(parameters, "printall", false);                 if (temp == "not found") { temp = "F"; }
+                       printAll = isTrue(temp);
+                       
                        temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
                        convert(temp, processors);
                        
@@ -217,6 +220,7 @@ int ChimeraSeqsCommand::execute(){
                chimera->setDivR(divR);
                chimera->setParents(parents);
                chimera->setMinSim(minSimilarity);
+               chimera->setPrint(printAll);
                
                                
                //find chimeras