testing metastats compile

diff --git a/metastats.h b/metastats.h
index ca8943a73b6485f34ea854e66201c9027b3e7441..2f3cc62ac380f9eb211ad9a86d63d84116387f03 100644 (file)
--- a/metastats.h
+++ b/metastats.h
@@ -33,7 +33,7 @@ void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *storage);
 void start(double *Imatrix,int *g,int *nr,int *nc,double *testing,
                        double storage[][9]);
 
-int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int);
+int metastat_main (char*, int, int, double, int, double**, int);
 
 #ifdef __cplusplus        
 }

diff --git a/mothur b/mothur
index f090f30ee6aa770553f0c67148e1d3915f91c298..ac8ea8a4afaf78fef42c97af9d14fb87ea7891b6 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 46081df5466b74ff03e9384cefcbee4ca82997a6..26969d81c7b6d95a0f7c603489be1da984ea7d99 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -590,42 +590,41 @@ void PipelineCommand::createPatsPipeline(){
                
                //sff.info command
                string thisCommand = "sffinfo(sff=" + sffFile + ")";
-               commands.push_back(thisCommand);
+               //commands.push_back(thisCommand);
                
                //trim.seqs command
                string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
                string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
-               thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=F, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
-               commands.push_back(thisCommand);
+               //thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=F, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
+               //commands.push_back(thisCommand);
                
                //unique.seqs
                string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";
                qualFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
                fastaFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
-               thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
-               commands.push_back(thisCommand);
+               //thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
+               //commands.push_back(thisCommand);
                
                //align.seqs
                string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
                fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
-               thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
-               commands.push_back(thisCommand);
+               //thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
+               //commands.push_back(thisCommand);
                
                //screen.seqs
                fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
-               thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + "group=" + groupFile + ", optimize=end-minlength)";
-               commands.push_back(thisCommand);
+               //thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
+       //      commands.push_back(thisCommand);
                
                //chimera.slayer
                fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
                nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
                groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
-               thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
-               commands.push_back(thisCommand);
+               //thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
+       //      commands.push_back(thisCommand);
                
                //remove.seqs
                string accnosFile = m->getRootName(m->getSimpleName(fastaFile))  + "slayer.accnos";
-               fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.chimeras";
                thisCommand = "remove.seqs(fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", accnos=" + accnosFile + ", dups=T)";
                commands.push_back(thisCommand);
                

diff --git a/unweighted.cpp b/unweighted.cpp
index da6ad2c1cc0bd6cea255546890b303888a46d6d7..edd628d82b72a871b6595aed0d1e644a7fd89af9 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -217,7 +217,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                        int lc = t->tree[i].getLChild();
                                        int rc = t->tree[i].getRChild();
                                        
-                                       //if yes, add to total your childrens branchLengths and your childrens tempTotals
+                                       //if yes, add your childrens tempTotals
                                        if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
                                                totalBL += tempTotals[lc] + tempTotals[rc]; 
                                                if (t->tree[i].getBranchLength() != -1) {
@@ -225,13 +225,12 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                                }else {
                                                        tempTotals[i] = 0.0;
                                                }
-                                               //tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
-                                       }else { //if no, your tempTotal is your childrens temp totals
+                                       }else { //if no, your tempTotal is your childrens temp totals + your branch length
                                                tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); 
                                        }
                                }
                        }
-                       
+       cout << UniqueBL << '\t' << totalBL << endl;            
                        UW = (UniqueBL / totalBL);  
        
                        if (isnan(UW) || isinf(UW)) { UW = 0; }
@@ -462,7 +461,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                        int lc = copyTree->tree[i].getLChild();
                                        int rc = copyTree->tree[i].getRChild();
                                        
-                                       //if yes, add to total your childrens branchLengths and your childrens tempTotals
+                                       //if yes, add your childrens tempTotals
                                        if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
                                                totalBL += tempTotals[lc] + tempTotals[rc]; 
                                                if (copyTree->tree[i].getBranchLength() != -1) {
@@ -470,8 +469,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                                }else {
                                                        tempTotals[i] = 0.0;
                                                }
-                                               //tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
-                                       }else { //if no, your tempTotal is your childrens temp totals
+                                       }else { //if no, your tempTotal is your childrens temp totals + your branch length
                                                tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
                                        }
                                }