fixed shhh.flows outputdir bug

diff --git a/calculator.h b/calculator.h
index 2c41329cff33ff7179054969a2595fcb53d2c717..6791d830f01c69492251b6110ebe5ba3d04a50a0 100644 (file)
--- a/calculator.h
+++ b/calculator.h
@@ -100,7 +100,7 @@ class BrokenStick
                void doBStick(vector<double>);
 };
 
-/**************************************************************************************************/
+//**************************************************************************************************/
 /*This Class calculates the geometric series distribution for the data.
 It prints the D-Statistic and the critical values for the Kolmogorov-Smirnov
 1-sample test at the 95% confidence interval.*/

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 32891c333ab5229aec50ed05ff5f03b6799d1396..d00ead8476ed226043b781edf680ac53a90e9a69 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1734,7 +1734,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
         outputNames.push_back(fastaFileName);
         
         if(compositeFASTAFileName != ""){
-            m->appendFiles(fastaFileName, compositeFASTAFileName);
+            m->appendFiles(fastaFileName, thisOutputDir + compositeFASTAFileName);
         }
     }
     catch(exception& e) {
@@ -1772,7 +1772,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
         
         
         if(compositeNamesFileName != ""){
-            m->appendFiles(nameFileName, compositeNamesFileName);
+            m->appendFiles(nameFileName, thisOutputDir + compositeNamesFileName);
         }              
     }
     catch(exception& e) {

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 86de668b4f57596bf11efb80807b18f932136551..0557c71bda3453068175fe3d405ff87972df80e1 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -392,8 +392,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
                
                while(moreSeqs) {
-                       //cout << "driver " << count << endl;
-       
+                               
                        if (m->control_pressed) { break; }
                        
                        int success = 1;

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 27bafd530cad4a66ef22e41696eef7e2328bde97..414c73cd1d2e6740b89d5200a5c7e7c704097ed6 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -59,9 +59,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;