all tests pass

src/windowMaker/windowMaker.cpp

@@ -104,14 +104,13 @@ void WindowMaker::MakeFixedSizeWindow(const BED& interval) {
 void WindowMaker::MakeFixedCountWindow(const BED& interval) {
     uint32_t interval_size = interval.end - interval.start ;
     uint32_t window_size = (interval_size-1)/_count + 1; // integer version of ceil(interval_size/_count)
-    uint32_t num_windows = CalculateWindows(interval);
 
     if (window_size==0 || interval_size==0)
         return;
 
     uint32_t i=1;
     for (uint32_t start = interval.start; start < interval.end; start += window_size, ++i) {
-        string name = GenerateID(interval, i, num_windows, _reverse);
+        string name = GenerateID(interval, i, _count, _reverse);
         uint32_t end = min(start + window_size,interval.end);
         cout << interval.chrom << "\t" << start << "\t" << end << name << endl;
     }

test/makewindows/test-makewindows.sh

@@ -11,7 +11,7 @@ check()
 
 
 ###########################################################
-#  Test forward window numbering 
+#  Test window size / forward window numbering 
 ############################################################
 echo "    makewindows.t01...\c"
 echo \
@@ -23,12 +23,11 @@ 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 
+#  Test window size / reverse window numbering 
 ############################################################
 echo "    makewindows.t02...\c"
 echo \
@@ -39,7 +38,91 @@ 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 -reverse -w 5000 -i winnum > obs
+check obs exp
+rm obs exp
 
+###########################################################
+#  Test window+step size / forward window numbering 
+############################################################
+echo "    makewindows.t03...\c"
+echo \
+"chr5	60000	65000	1
+chr5	62000	67000	2
+chr5	64000	69000	3
+chr5	66000	70000	4
+chr5	68000	70000	5
+chr5	73000	78000	1
+chr5	75000	80000	2
+chr5	77000	82000	3
+chr5	79000	84000	4
+chr5	81000	86000	5
+chr5	83000	88000	6
+chr5	85000	90000	7
+chr5	87000	90000	8
+chr5	89000	90000	9
+chr5	100000	101000	1" > exp
+$BT makewindows -b input.bed -w 5000 -s 2000 -i winnum > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test window size / reverse window numbering 
+############################################################
+echo "    makewindows.t04...\c"
+echo \
+"chr5	60000	65000	5
+chr5	62000	67000	4
+chr5	64000	69000	3
+chr5	66000	70000	2
+chr5	68000	70000	1
+chr5	73000	78000	9
+chr5	75000	80000	8
+chr5	77000	82000	7
+chr5	79000	84000	6
+chr5	81000	86000	5
+chr5	83000	88000	4
+chr5	85000	90000	3
+chr5	87000	90000	2
+chr5	89000	90000	1
+chr5	100000	101000	1" > exp
+$BT makewindows -b input.bed -reverse -w 5000 -s 2000 -i winnum > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+#  Test fixed size / forward window numbering 
+############################################################
+echo "    makewindows.t05...\c"
+echo \
+"chr5	60000	63334	1
+chr5	63334	66668	2
+chr5	66668	70000	3
+chr5	73000	78667	1
+chr5	78667	84334	2
+chr5	84334	90000	3
+chr5	100000	100334	1
+chr5	100334	100668	2
+chr5	100668	101000	3" > exp
+$BT makewindows -n 3 -b input.bed -i winnum > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test fixed size / reverse window numbering 
+############################################################
+echo "    makewindows.t06...\c"
+echo \
+"chr5	60000	63334	3
+chr5	63334	66668	2
+chr5	66668	70000	1
+chr5	73000	78667	3
+chr5	78667	84334	2
+chr5	84334	90000	1
+chr5	100000	100334	3
+chr5	100334	100668	2
+chr5	100668	101000	1" > exp
+$BT makewindows -n 3 -b input.bed -reverse -i winnum > obs
 check obs exp
 rm obs exp