Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 15 Sep 2016 22:26:26 +0200
Description: There is a dir bin/ containing some R files which
 is removed in clean target.  Just use a different output dir
 that can be cleaned without problems

--- a/Makefile
+++ b/Makefile
@@ -15,7 +15,7 @@ SOURCES = src/Variant.cpp \
 OBJECTS= $(SOURCES:.cpp=.o)
 
 VCF_LIB_LOCAL:=$(shell pwd)
-BIN_DIR:=bin
+BIN_DIR:=binaries
 LIB_DIR:=lib
 SRC_DIR=src
 INC_DIR:=include
@@ -115,7 +115,7 @@ BIN_SOURCES = src/vcfecho.cpp \
 # src/vcfsom.cpp
 
 #BINS = $(BIN_SOURCES:.cpp=)
-BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
+BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
 SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
 
 # TABIX = tabixpp/tabix.o
@@ -183,7 +183,7 @@ $(FILEVERCMP): pre
 	ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
 
 $(SHORTBINS): pre
-	$(MAKE) bin/$@
+	$(MAKE) $(BIN_DIR)/$@
 
 $(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
