removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 394172c34cc80feaa85f4ced1b6883d63058bb87..b94d4450e321df7af165cdcf917de1e7cd7d1a02 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -14,7 +14,7 @@
 //**********************************************************************************************************************
 vector<string> ChimeraSlayerCommand::getValidParameters(){     
        try {
-               string AlignArray[] =  {"fasta", "processors", "name","window", "template","numwanted", "ksize", "match","mismatch", 
+               string AlignArray[] =  {"fasta", "processors", "name","window", "include","template","numwanted", "ksize", "match","mismatch", 
                        "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
                vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                return myArray;
@@ -69,7 +69,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "processors","name", "window", "template","numwanted", "ksize", "match","mismatch", 
+                       string Array[] =  {"fasta", "processors","name", "include","window", "template","numwanted", "ksize", "match","mismatch", 
                        "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
@@ -231,6 +231,9 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
                        convert(temp, processors);
                        
+                       includeAbunds = validParameter.validFile(parameters, "include", false);         if (includeAbunds == "not found") { includeAbunds = "greater"; }
+                       if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); }
+                       
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
                        convert(temp, ksize);
                                                
@@ -346,7 +349,7 @@ int ChimeraSlayerCommand::execute(){
                                chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);   
                        }else {
                                if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
-                                       chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, nameFileNames[s], search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); 
+                                       chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);  
                                }else {
                                        
                                        m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -368,7 +371,7 @@ int ChimeraSlayerCommand::execute(){
                                        string nameFile = filenames["name"][0];
                                        fastaFileNames[s] = filenames["fasta"][0];
                        
-                                       chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, nameFile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); 
+                                       chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, nameFile, search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);  
                                }
                        }