4a1d781b5b32ec620f92d8359326fc97822aed55
hiram
  Tue May 1 10:42:15 2012 -0700
after all these years, gsBig has been leaving garbage all over the place for no good reason.  Fixed this bug
diff --git src/hg/gsBig/gsBig.c src/hg/gsBig/gsBig.c
index c574d2d..da30028 100644
--- src/hg/gsBig/gsBig.c
+++ src/hg/gsBig/gsBig.c
@@ -674,41 +674,41 @@
 		}
 	    else
 		{
 		faWrite(tempFa, "split", seq.dna + offset, sizeOne); 
 		dyStringClear(dy);
 		dyStringPrintf(dy, "%s %s %s", exePath, parPath, tempFa);
 		if (suboptName != NULL)
 		    dyStringPrintf(dy, " -subopt");
 		dyStringPrintf(dy, " > %s", tempGs);
 		verbose(3, "%s\n", dy->string);
 		mustSystem(dy->string);
 		seg = parseSegment(tempGs, offset, offset+sizeOne, NULL);
 		slAddHead(&segList, seg);
 		}
 	    chunkNum++;
+            if (! optionExists("noRemove"))
+                {
+                remove(tempFa);
+                remove(tempGs);
+                }
 	    }
 	slReverse(&segList);
 	seg = mergeSegs(segList);
 	writeSeg(seqName, seg, gtfFile, subFile, transFile);
 	freez(&seqName);
 	}
-    if (! optionExists("noRemove"))
-	{
-	remove(tempFa);
-	remove(tempGs);
-	}
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc < 3)
     usage();
 winSize = optionInt("window", winSize);
 stepSize = 2*winSize/3;
 gsBig(argv[1], argv[2], 
 	optionVal("subopt", NULL),
 	optionVal("trans", NULL),
 	optionVal("exe", NULL),