test stubs; ``-n`` is excepting now

src/windowMaker/windowMakerMain.cpp

@@ -98,9 +98,6 @@ int windowmaker_main(int argc, char* argv[]) {
                 i++;
             }
         }
-        else if(PARAMETER_CHECK("-reverse", 8, parameterLength)) {
-            reverse = true;
-        }
         else if(PARAMETER_CHECK("-i", 2, parameterLength)) {
             if ((i+1) < argc) {
                 if (strcmp(argv[i+1],"winnum")==0)
@@ -116,6 +113,9 @@ int windowmaker_main(int argc, char* argv[]) {
                 i++;
             }
         }
+        else if(PARAMETER_CHECK("-reverse", 8, parameterLength)) {
+            reverse = true;
+        }
         else {
             cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
             showHelp = true;

test/makewindows/test-makewindows.sh

@@ -11,11 +11,35 @@ check()
 
 
 ###########################################################
-#  Test forward and reverse window numbering 
+#  Test forward window numbering 
 ############################################################
 echo "    makewindows.t01...\c"
-echo
+echo \
+"chr5	60000	65000	1
+chr5	65000	70000	2
+chr5	73000	78000	1
+chr5	78000	83000	2
+chr5	83000	88000	3
+chr5	88000	90000	4
+chr5	100000	101000	1" > exp
+$BT makewindows -b input.bed -w 5000  -i winnum > obs
+
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test reverse window numbering 
+############################################################
+echo "    makewindows.t02...\c"
+echo \
+"chr5	60000	65000	2
+chr5	65000	70000	1
+chr5	73000	78000	4
+chr5	78000	83000	3
+chr5	83000	88000	2
+chr5	88000	90000	1
+chr5	100000	101000	1" > exp
+$BT makewindows -b input.bed -reverse -w 5000  -i winnum > obs
 
-$BT makewindows -b input.bed -w 500 -i winnum > obs
 check obs exp
 rm obs exp