Merge remote-tracking branch 'mothur/master'

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 82e1228606986b18d7176a5cdf70e84a83cb695f..ee43bcbf72a2ca00af3e2270768f34ac1357bb71 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -15,6 +15,7 @@
 #include "chimera.h"
 #include "chimeraslayer.h"
 #include "sequenceparser.h"
+#include "sequencecountparser.h"
 
 /***********************************************************/
 
@@ -27,8 +28,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    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"; }
        
@@ -51,12 +53,14 @@ private:
        int divideInHalf(Sequence, string&, string&);
        map<string, int> sortFastaFile(string, string);
        map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+    int sortFastaFile(vector<Sequence>&, map<string, int>&, string newFile);
        string getNamesFile(string&);
        //int setupChimera(string,);
        int MPIExecute(string, string, string, string, map<string, int>&);
-       int deconvoluteResults(SequenceParser*, string, string, string);
+       int deconvoluteResults(map<string, string>&, string, string, string);
        map<string, int> priority;
        int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+    int setUpForSelfReference(SequenceCountParser*&, map<string, string>&, map<string, map<string, int> >&, int);
        int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
        int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
        int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
@@ -66,8 +70,8 @@ private:
        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;
-       string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
+       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;
        
@@ -209,8 +213,6 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                        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()) { 
@@ -223,7 +225,7 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                
                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;   }
@@ -314,18 +316,18 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                                        
                                        
                                }
-                               count++;
+                               pDataArray->count++;
                        }
                        
                        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
-               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();
-               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();