added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index c40963999f953e2cfc534afcfdaec1a1e56b8c72..fe0685bea19678213fa0ddb8ccfade9ad08c4b12 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -776,8 +776,8 @@ int ShhherCommand::execute(){
 
                
                if(compositeFASTAFileName != ""){
-                       outputNames.push_back(compositeFASTAFileName);
-                       outputNames.push_back(compositeNamesFileName);
+                       outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName); 
                }
 
                m->mothurOutEndLine();
@@ -1743,7 +1743,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
             }
         }
         qualityFile.close();
-        outputNames.push_back(qualityFileName);
+        outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
         
     }
     catch(exception& e) {
@@ -1788,7 +1788,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
         }
         fastaFile.close();
         
-        outputNames.push_back(fastaFileName);
+        outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
         
         if(compositeFASTAFileName != ""){
             m->appendFiles(fastaFileName, compositeFASTAFileName);
@@ -1825,7 +1825,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
             }
         }
         nameFile.close();
-        outputNames.push_back(nameFileName);
+        outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
         
         
         if(compositeNamesFileName != ""){
@@ -1857,7 +1857,7 @@ void ShhherCommand::writeGroups(){
             groupFile << seqNameVector[i] << '\t' << fileGroup << endl;
         }
         groupFile.close();
-        outputNames.push_back(groupFileName);
+        outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
         
     }
     catch(exception& e) {
@@ -1917,7 +1917,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
             }
         }
         otuCountsFile.close();
-        outputNames.push_back(otuCountsFileName);
+        outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
         
     }
     catch(exception& e) {
@@ -1948,8 +1948,8 @@ int ShhherCommand::execute(){
 #endif
         
                if(compositeFASTAFileName != ""){
-                       outputNames.push_back(compositeFASTAFileName);
-                       outputNames.push_back(compositeNamesFileName);
+                       outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName);
                }
 
                m->mothurOutEndLine();
@@ -3266,7 +3266,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                        }
                }
                qualityFile.close();
-               outputNames.push_back(qualityFileName);
+               outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
         
        }
        catch(exception& e) {
@@ -3310,7 +3310,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU
                }
                fastaFile.close();
         
-               outputNames.push_back(fastaFileName);
+               outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
         
                if(thisCompositeFASTAFileName != ""){
                        m->appendFiles(fastaFileName, thisCompositeFASTAFileName);
@@ -3345,7 +3345,7 @@ void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, s
                        }
                }
                nameFile.close();
-               outputNames.push_back(nameFileName);
+               outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
                
                
                if(thisCompositeNamesFileName != ""){
@@ -3370,7 +3370,7 @@ void ShhherCommand::writeGroups(string groupFileName, string fileRoot, int numSe
                        groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
                }
                groupFile.close();
-               outputNames.push_back(groupFileName);
+               outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
         
        }
        catch(exception& e) {
@@ -3429,7 +3429,7 @@ void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int num
                        }
                }
                otuCountsFile.close();
-               outputNames.push_back(otuCountsFileName);
+               outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
         
        }
        catch(exception& e) {