added check for blank files in openInputFile, add check for groupfiles that contain...

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 7b99cab9e7eed714a0cefeee4b45ed8057429c6f..5f575f2bc41721e7fc3b52ec7d6fb68163b43131 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -146,18 +146,15 @@ void Pintail::getChimeras() {
                        mothurOut("Done."); mothurOutEndLine();
                }else {         createProcessesPairs();         }
                
-/*string o = "foronlinepintailpairs-eachgap";
+string o = "closestmatch.eachgap.fasta";
 ofstream out7;
 openOutputFile(o, out7);
 
 for (int i = 0; i < bestfit.size(); i++) {
-       out7 << querySeqs[i]->getName() << endl;
-       out7 << querySeqs[i]->getUnaligned() << endl << endl;
-       
-       out7 << bestfit[i]->getName() << endl;
-       out7 << bestfit[i]->getUnaligned() << endl << endl << endl;
+       out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+       out7 << bestfit[i]->getAligned() << endl;
 }              
-out7.close();/*/       
+out7.close();  
                //find P
                mothurOut("Getting conservation... "); cout.flush();
                if (consfile == "") {