From a43e8f6898727e19ed95b15d4b7ebe98ea84035b Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 16 Nov 2011 13:24:28 -0500
Subject: [PATCH] Makefile tweak.
---
src/Makefile | 48 -----------------------------------------
src/bedpeToBam/Makefile | 7 +++---
2 files changed, 4 insertions(+), 51 deletions(-)
delete mode 100644 src/Makefile
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index eead49f8..00000000
--- a/src/Makefile
+++ /dev/null
@@ -1,48 +0,0 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
-
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/version/ \
- -I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/BamTools/include
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= multiCovMain.cpp multiCovBam.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= multiCovBam
-
-all: $(PROGRAM)
-
-.PHONY: all
-
-$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
- @echo " * linking $(PROGRAM)"
- @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
-
-$(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-
-clean:
- @echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
-.PHONY: clean
diff --git a/src/bedpeToBam/Makefile b/src/bedpeToBam/Makefile
index f6e18c0c..b2f7d128 100644
--- a/src/bedpeToBam/Makefile
+++ b/src/bedpeToBam/Makefile
@@ -6,6 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+ -I$(UTILITIES_DIR)/bedFilePE/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/genomeFile/ \
@@ -17,12 +18,12 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= bedToBam.cpp
+SOURCES= bedpeToBam.cpp
OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
+_EXT_OBJECTS=bedFile.o bedFilePE.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= bedToBam
+PROGRAM= bedpeToBam
all: $(PROGRAM)
--
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