added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index ce7ce456d87c5c8c6e5a137cd661b02710e0977c..9a25582ddad078665bbc3f7e098dc4cbcf047097 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -23,6 +23,7 @@ vector<string> ChimeraUchimeCommand::setParameters(){
         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
                CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+        CommandParameter pstrand("strand", "String", "", "", "", "", "","",false,false); parameters.push_back(pstrand);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                CommandParameter pabskew("abskew", "Number", "", "1.9", "", "", "","",false,false); parameters.push_back(pabskew);
@@ -61,7 +62,7 @@ string ChimeraUchimeCommand::getHelpString(){
                string helpString = "";
                helpString += "The chimera.uchime command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
                helpString += "This command is a wrapper for uchime written by Robert C. Edgar.\n";
-               helpString += "The chimera.uchime command parameters are fasta, name, count, reference, processors, dereplicate, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl and queryfact.\n";
+               helpString += "The chimera.uchime command parameters are fasta, name, count, reference, processors, dereplicate, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl, strand and queryfact.\n";
                helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
                helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
         helpString += "The count parameter allows you to provide a count file, if you are using template=self. \n";
@@ -543,6 +544,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        maxp = validParameter.validFile(parameters, "maxp", false);                                             if (maxp == "not found")                        { useMaxp = false; maxp = "2";                                          }       else{ useMaxp = true;                   }
                        minlen = validParameter.validFile(parameters, "minlen", false);                                 if (minlen == "not found")                      { useMinlen = false; minlen = "10";                                     }       else{ useMinlen = true;                 }
                        maxlen = validParameter.validFile(parameters, "maxlen", false);                                 if (maxlen == "not found")                      { useMaxlen = false; maxlen = "10000";                          }       else{ useMaxlen = true;                 }
+            
+            strand = validParameter.validFile(parameters, "strand", false);    if (strand == "not found")      {  strand = ""; }
                        
                        temp = validParameter.validFile(parameters, "ucl", false);                                              if (temp == "not found") { temp = "f"; }
                        ucl = m->isTrue(temp);
@@ -1232,6 +1235,15 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                        *tempa = '\0'; strncat(tempa, alns.c_str(), alns.length());
                        cPara.push_back(tempa);
                }
+        
+        if (strand != "") {
+                       char* tempA = new char[9]; 
+                       *tempA = '\0'; strncat(tempA, "--strand", 8);
+                       cPara.push_back(tempA);
+                       char* tempa = new char[strand.length()+1];
+                       *tempa = '\0'; strncat(tempa, strand.c_str(), strand.length());
+                       cPara.push_back(tempa);
+               }
                
                if (useAbskew) {
                        char* tempskew = new char[9];
@@ -1631,7 +1643,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                        
                        uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0,  i);
                        tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
-                       tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+                       tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, strand);
                        
                        pDataArray.push_back(tempUchime);
                        processIDS.push_back(i);
@@ -1763,7 +1775,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
                        
                        uchimeData* tempUchime = new uchimeData(outputFName+extension, uchimeLocation, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
                        tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
-                       tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+                       tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, strand);
                        
                        pDataArray.push_back(tempUchime);
                        processIDS.push_back(i);