diff --git a/Makefile b/Makefile
index 51768e86ca94e939dba5657c6f8246d8dfa40991..39dc39d57b9b18f4c90120a45e69f7d4cfdbce23 100644
--- a/Makefile
+++ b/Makefile
@@ -22,7 +22,7 @@ export CXX ?= g++
 #include includes/$(BLD_PLATFORM).inc
 
 # define our source subdirectories
-SUBDIRS = $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed
+SUBDIRS = $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed
 
 UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
 all: