--- a/tools/mira4/mira4.py	Tue Jun 10 10:11:58 2014 -0400
+++ b/tools/mira4/mira4.py	Tue Oct 28 08:29:59 2014 -0400
@@ -58,6 +58,9 @@
 parser.add_option("--log", dest="log",
                   default="-", metavar="FILE",
                   help="MIRA logging output filename")
+parser.add_option("-v", "--version", dest="version",
+                  default=False, action="store_true",
+                  help="Show version and quit")
 options, args = parser.parse_args()
 manifest = options.manifest
 out_maf = options.maf
@@ -84,7 +87,7 @@
 mira_convert_ver = get_version(mira_convert)
 if not mira_convert_ver.strip().startswith("4.0"):
     stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
-if "-v" in sys.argv or "--version" in sys.argv:
+if options.version:
     print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
     if mira_ver != mira_convert_ver:
         print "WARNING: miraconvert %s" % mira_convert_ver
@@ -192,7 +195,11 @@
     #For mapping mode, probably most people would expect a BAM file
     #using the reference FASTA file...
     if out_bam and out_bam != "-":
-        msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
+        if out_maf and out_maf != "-":
+            msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
+        else:
+            #Not collecting the MAF file, use original location        
+            msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
         if msg:
             stop_err(msg)
 
@@ -216,7 +223,9 @@
 
 assert os.path.isdir(temp)
 d = "%s_assembly" % name
-assert not os.path.isdir(d), "Path %s already exists" % d
+#This can fail on my development machine if stale folders exist
+#under Galaxy's .../database/job_working_directory/ tree:
+assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d))
 try:
     #Check path access
     os.mkdir(d)