pcr.seqs bug fix. working on shannon range calc

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index a1eae4687c4d49b2ce8e0f90895a36a994aec689..6a4df6388683b1cda6aa5aa41d1ec3d2d672a15f 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -575,7 +575,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
         
         
 
-        if (fileAligned) {
+        if (fileAligned && adjustNeeded) {
             //find pend - pend is the biggest ending value, but we must account for when we adjust the start.  That adjustment may make the "new" end larger then the largest end. So lets find out what that "new" end will be.
             ifstream inLocations;
             m->openInputFile(locationsFile, inLocations);
@@ -608,7 +608,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
             inLocations.close();
             
             adjustDots(goodFileName, locationsFile, pstart, pend);
-        }
+        }else { m->mothurRemove(locationsFile); }
         
         return num;