test stub; refactor num_window calculation

src/windowMaker/windowMaker.cpp

@@ -78,9 +78,18 @@ void WindowMaker::MakeBEDWindow(const BED& interval)
         MakeFixedCountWindow(interval);
 }
 
+uint32_t WindowMaker::CalculateWindows(const BED& interval) {
+    uint32_t num_windows = (interval.end - interval.start) / _step;
+    if ((interval.end - interval.start) % _step > 0) {
+        // add 1 to num_windows if the last window is less than _step 
+        num_windows += 1;
+    }
+    return num_windows;
+}
 void WindowMaker::MakeFixedSizeWindow(const BED& interval) {
     uint32_t i=1;
-    uint32_t num_windows = (interval.end - interval.start) / _step;
+    uint32_t num_windows = CalculateWindows(interval);
+
     for (uint32_t start = interval.start; start <= interval.end; start += _step, ++i) {
         string name = GenerateID(interval, i, num_windows, _reverse);
         if ((start + _size) <= interval.end) {
@@ -95,7 +104,8 @@ 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 = interval_size / window_size;
+    uint32_t num_windows = CalculateWindows(interval);
+
     if (window_size==0 || interval_size==0)
         return;
 
@@ -109,19 +119,21 @@ void WindowMaker::MakeFixedCountWindow(const BED& interval) {
 
 string WindowMaker::GenerateID(const BED& interval, uint32_t window_index, uint32_t num_windows, bool _reverse) const {
     stringstream s;
+    // cout << "num_windows: " << num_windows << endl;
+    // cout << "window_index: " << window_index << endl << endl;
     switch(_id_method) {
     case ID_SOURCE_ID:
          s << "\t" << interval.name;
          break;
     case ID_WINDOW_NUMBER:
-         if (_reverse == true) {
+         if (_reverse == true && num_windows > 0) {
             s << "\t" << num_windows - window_index + 1;
          } else {
             s << "\t" << window_index;
          }
          break;
     case ID_SOURCE_ID_WINDOW_NUMBER:
-         if (_reverse == true) {
+         if (_reverse == true && num_windows > 0) {
             s << "\t" << interval.name << "_" << num_windows - window_index + 1;
          } else {
             s << "\t" << interval.name << "_" << window_index;

src/windowMaker/windowMaker.h

@@ -58,6 +58,7 @@ private:
 
     void MakeFixedSizeWindow(const BED& interval);
     void MakeFixedCountWindow(const BED& interval);
+    uint32_t CalculateWindows(const BED& interval);
 
     string GenerateID(const BED& interval, uint32_t window_index, uint32_t num_windows, bool _reverse) const;
 };

test/makewindows/input.bed

+chr5	60000	70000	AAA
+chr5	73000	90000	BBB
+chr5	100000	101000	CCC
+

test/makewindows/test-makewindows.sh

+BT=${BT-../../bin/bedtools}
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+    	echo fail
+	fi
+}
+
+
+###########################################################
+#  Test forward and reverse window numbering 
+############################################################
+echo "    makewindows.t01...\c"
+echo
+
+$BT makewindows -b input.bed -w 500 -i winnum > obs
+check obs exp
+rm obs exp