Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 26 May 2020 15:07:58 +0200
Description: Use Debian packaged libraries
 Please note: lumpy-sv contains a code copy of bedtools.  Unfortunately
 bedtools does not have a development library so its hard to replace this
 code copy here.

--- a/Makefile
+++ b/Makefile
@@ -24,21 +24,18 @@
 #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC 
 export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC 
 export LIBS		= -lz -L $(ZLIB_PATH)
-export BT_ROOT  = src/utils/BamTools/
+#export BT_ROOT  = src/utils/BamTools/
 export MKFILE_DIR = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 
 SUBDIRS = $(SRC_DIR)/lumpy
 
 UTIL_SUBDIRS =	$(SRC_DIR)/utils/bedFile \
 				$(SRC_DIR)/utils/version \
-				$(SRC_DIR)/utils/gzstream \
 				$(SRC_DIR)/utils/fileType \
 				$(SRC_DIR)/utils/bedFilePE \
 				$(SRC_DIR)/utils/genomeFile \
-				$(SRC_DIR)/utils/BamTools \
 				$(SRC_DIR)/utils/BamTools-Ancillary \
 				$(SRC_DIR)/utils/sequenceUtilities \
-				$(SRC_DIR)/utils/sqlite3
 
 
 all:	lumpy_filter lumpyexpress lumpy
@@ -50,9 +47,9 @@
 	@echo "Building lumpy:"
 	@echo "========================================================="
 
-	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
+	#$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
 
-	@for dir in $(UTIL_SUBDIRS); do \
+	for dir in $(UTIL_SUBDIRS); do \
 		echo "- Building in $$dir"; \
 		$(MAKE) --no-print-directory -C $$dir; \
 		echo ""; \
@@ -64,7 +61,7 @@
 		echo ""; \
 	done
 
-lumpy_filter: htslib
+lumpy_filter: # htslib - use Debian packaged htslib
 	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
 	$(MAKE) --no-print-directory -C src/filter/
 	cp src/filter/lumpy_filter $(BIN_DIR)
@@ -100,9 +97,9 @@
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-	@rm -Rf $(BT_ROOT)/lib
-	@rm -f $(BT_ROOT)/src/api/*.o
-	@rm -f $(BT_ROOT)/src/api/internal/*.o
-	@rm -Rf $(BT_ROOT)/include
+	#rm -Rf $(BT_ROOT)/lib
+	#rm -f $(BT_ROOT)/src/api/*.o
+	#rm -f $(BT_ROOT)/src/api/internal/*.o
+	#rm -Rf $(BT_ROOT)/include
 
 .PHONY: clean
--- a/src/lumpy/Makefile
+++ b/src/lumpy/Makefile
@@ -9,14 +9,13 @@
            -I$(UTILITIES_DIR)/bedFilePE/ \
            -I$(UTILITIES_DIR)/genomeFile/ \
            -I$(UTILITIES_DIR)/version/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
-           -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+           -I/usr/include/bamtools \
+	   -I$(UTILITIES_DIR)/BamTools-Ancillary \
            -I$(UTILITIES_DIR)/sequenceUtilities \
            -I$(UTILITIES_DIR)/UCSCBins \
-           -I$(UTILITIES_DIR)/sqlite3 
+	   -I/usr/include/fastahack
 
 # ----------------------------------
 # define our source and object files
@@ -39,12 +38,10 @@
 OBJECTS= $(SOURCES:.cpp=.o)
 _EXT_OBJECTS=BamAncillary.o \
 			 sequenceUtils.o \
-			 gzstream.o \
 			 bedFilePE.o \
 			 bedFile.o \
 			 genomeFile.o \
-			 fileType.o \
-			 sqlite3.o 
+			 fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM=lumpy
@@ -54,24 +51,25 @@
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ \
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ \
 		-L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools \
 		$(LIBS) \
-		-lz -lm -ldl -lpthread
+		-lgzstream -lz -lm -ldl -lpthread
 
 $(OBJ_DIR)/%.o: %.cpp
 	@echo "  * compiling" $<
-	@$(CXX) -g  -c $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
+	$(CXX) -g  -c $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
 
 $(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ 
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sqlite3/ 
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ 
+	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sqlite3/
+	echo "Use Debian packaged bamtools bedtools gzstream and sqlite3"
 
 clean:
 	@echo "Cleaning up."
--- a/src/filter/Makefile
+++ b/src/filter/Makefile
@@ -1,4 +1,4 @@
 
 all:
-	$(CC) -I../../lib/htslib/ -o lumpy_filter filter.c ../../lib/htslib/libhts.a -lcrypto -lcurl -lpthread -lz
+	$(CC) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
 
--- a/src/utils/genomeFile/Makefile
+++ b/src/utils/genomeFile/Makefile
@@ -6,7 +6,7 @@
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
-           -I$(UTILITIES_DIR)/BamTools/include/	
+           -I/usr/include/bamtools
 
 # ----------------------------------
 # define our source and object files
--- a/src/utils/BamTools-Ancillary/Makefile
+++ b/src/utils/BamTools-Ancillary/Makefile
@@ -2,10 +2,9 @@
 BIN_DIR = ../../../bin/
 UTILITIES_DIR = ../
 
-INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
+INCLUDES = -I/usr/include/bamtools \
            -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/
 
 # ----------------------------------
@@ -27,4 +26,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- a/src/utils/BlockedIntervals/Makefile
+++ b/src/utils/BlockedIntervals/Makefile
@@ -2,9 +2,8 @@
 BIN_DIR = ../../../bin/
 UTILITIES_DIR = ../
 
-INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
+INCLUDES = -I/usr/include/bamtools \
            -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/
 
@@ -13,7 +12,7 @@
 # ----------------------------------
 SOURCES= BlockedIntervals.cpp BlockedIntervals.h
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o fileType.o gzstream.o
+_EXT_OBJECTS=bedFile.o fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
@@ -32,4 +31,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- a/src/utils/bedFile/Makefile
+++ b/src/utils/bedFile/Makefile
@@ -5,7 +5,6 @@
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/stringUtilities/
 
@@ -14,7 +13,7 @@
 # ----------------------------------
 SOURCES= bedFile.cpp bedFile.h
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o
+_EXT_OBJECTS=lineFileUtilities.o fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
@@ -29,4 +28,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- a/src/utils/bedGraphFile/Makefile
+++ b/src/utils/bedGraphFile/Makefile
@@ -13,7 +13,7 @@
 # ----------------------------------
 SOURCES= bedGraphFile.cpp bedGraphFile.h
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o
+_EXT_OBJECTS=lineFileUtilities.o fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
--- a/src/utils/tabFile/Makefile
+++ b/src/utils/tabFile/Makefile
@@ -5,7 +5,6 @@
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/
 
 # ----------------------------------
@@ -13,7 +12,7 @@
 # ----------------------------------
 SOURCES= tabFile.cpp tabFile.h
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=lineFileUtilities.o gzstream.o fileType.o
+_EXT_OBJECTS=lineFileUtilities.o fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
@@ -28,4 +27,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean