mupa for test case

this is used to verify that the mussa tosses a useful exception
when someone sets a bad filename for an annotation.

diff --git a/examples/directory.mupa b/examples/directory.mupa
new file mode 100644 (file)
index 0000000..f57d81b
--- /dev/null
+++ b/examples/directory.mupa
@@ -0,0 +1,28 @@
+#
+# Used to make sure that we properly report an error when
+# an annotation is not a file.
+# 
+
+
+# name of anaylsis directory and stem for associated files
+ANA_NAME directory
+
+# if APPEND vars true, a _wXX and/or _tYY added to analysis name
+# where XX = WINDOW and YY = THRESHOLD
+# Highly recommeded with use of command line override of WINDOW or THRESHOLD
+APPEND_WIN true
+APPEND_THRES true
+  
+# first sequence info
+SEQUENCE seq/mouse_mck_pro.fa
+ANNOTATION mm_mck3test.annot
+SEQ_START 300
+
+# the second sequence info
+SEQUENCE seq/human_mck_pro.fa
+ANNOTATION seq
+SEQ_START 300
+
+# analyses parameters: command line args -w -t will override these
+WINDOW 30
+THRESHOLD 20