X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=prcseqscommand.cpp;h=6a4df6388683b1cda6aa5aa41d1ec3d2d672a15f;hp=a1eae4687c4d49b2ce8e0f90895a36a994aec689;hb=a65438a717aba8cad1ff86c53279b191710b8810;hpb=9a808b553f14a25f9c5e94da92a7077a57054e8e

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index a1eae46..6a4df63 100644
--- 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;