added trim overlap parameter to make.contigs

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 93adb7bf53b280892715411c66aedcf15b5c0df3..ee43bcbf72a2ca00af3e2270768f34ac1357bb71 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -28,9 +28,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }

-       string getOutputFileNameTag(string, string);
+       

        string getHelpString(); 
        string getHelpString(); 

-       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+    string getOutputPattern(string);   
+       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }

        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 


@@ -69,7 +70,7 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
        #endif
 
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
        #endif
 

-       bool abort, realign, trim, trimera, save, hasName, hasCount;
+       bool abort, realign, trim, trimera, save, hasName, hasCount, dups;

        string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;


@@ -212,8 +213,6 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                        inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
                }
                
                        inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
                }
                

-               pDataArray->count = pDataArray->end;
-               

                if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera;  return 0;    }
                
                if (chimera->getUnaligned()) { 
                if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera;  return 0;    }
                
                if (chimera->getUnaligned()) { 


@@ -226,7 +225,7 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                
                if (pDataArray->start == 0) { chimera->printHeader(out); }
                
                
                if (pDataArray->start == 0) { chimera->printHeader(out); }
                

-               int count = 0;
+               pDataArray->count = 0;

                for(int i = 0; i < pDataArray->end; i++){
                        
                        if (pDataArray->m->control_pressed) {   out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 1;   }
                for(int i = 0; i < pDataArray->end; i++){
                        
                        if (pDataArray->m->control_pressed) {   out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 1;   }


@@ -317,18 +316,18 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                                        
                                        
                                }
                                        
                                        
                                }

-                               count++;
+                               pDataArray->count++;

                        }
                        
                        delete candidateSeq;
                        //report progress
                        }
                        
                        delete candidateSeq;
                        //report progress

-                       if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }

                }
                //report progress
                }
                //report progress

-               if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }

                
                pDataArray->numNoParents = chimera->getNumNoParents();
                
                pDataArray->numNoParents = chimera->getNumNoParents();

-               if (pDataArray->numNoParents == count) {        pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
+               if (pDataArray->numNoParents == pDataArray->count) {    pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }

 
                out.close();
                out2.close();
 
                out.close();
                out2.close();