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R3
legacy
bedtools2
Commits
2d7b5503
Commit
2d7b5503
authored
Jul 15, 2015
by
arq5x
Browse files
resolve conflict
parents
b1e3d8de
833bd238
Changes
67
Hide whitespace changes
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Makefile
View file @
2d7b5503
...
...
@@ -134,8 +134,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
all
:
print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
@
echo
"- Building main bedtools binary."
@
$(CXX)
$(CXXFLAGS)
-c
src/bedtools.cpp
-o
obj/bedtools.o
$(INCLUDES)
@
$(CXX)
$(CXXFLAGS)
-o
$(BIN_DIR)
/bedtools
$(BUILT_OBJECTS)
-L
$(UTIL_DIR)
/BamTools/lib/
-lbamtools
$(LIBS)
$(LDFLAGS)
$(INCLUDES)
@
$(CXX)
$(CXXFLAGS)
$(CPPFLAGS)
-c
src/bedtools.cpp
-o
obj/bedtools.o
$(INCLUDES)
@
$(CXX)
$(CXXFLAGS)
$(CPPFLAGS)
-o
$(BIN_DIR)
/bedtools
$(BUILT_OBJECTS)
-L
$(UTIL_DIR)
/BamTools/lib/
-lbamtools
$(LIBS)
$(LDFLAGS)
$(INCLUDES)
@
echo
"done."
@
echo
"- Creating executables for old CLI."
...
...
src/annotateBed/Makefile
View file @
2d7b5503
...
...
@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
...
...
src/bamToBed/Makefile
View file @
2d7b5503
...
...
@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/bamToFastq/Makefile
View file @
2d7b5503
...
...
@@ -24,7 +24,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/bed12ToBed6/Makefile
View file @
2d7b5503
...
...
@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/bedToBam/Makefile
View file @
2d7b5503
...
...
@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/bedToIgv/Makefile
View file @
2d7b5503
...
...
@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/bedpeToBam/Makefile
View file @
2d7b5503
...
...
@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
$(EXT_OBJECTS)
:
@
$(MAKE)
--no-print-directory
-C
$(UTILITIES_DIR)
/BamTools/
...
...
src/closestFile/Makefile
View file @
2d7b5503
...
...
@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/clusterBed/Makefile
View file @
2d7b5503
...
...
@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/expand/Makefile
View file @
2d7b5503
...
...
@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/fastaFromBed/Makefile
View file @
2d7b5503
...
...
@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/fisher/Makefile
View file @
2d7b5503
...
...
@@ -51,7 +51,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(DFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(DFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/flankBed/Makefile
View file @
2d7b5503
...
...
@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/genomeCoverageBed/Makefile
View file @
2d7b5503
...
...
@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/getOverlap/Makefile
View file @
2d7b5503
...
...
@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
...
...
src/groupBy/Makefile
View file @
2d7b5503
...
...
@@ -25,7 +25,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I
$(UTILITIES_DIR)
/version/
\
-I
$(UTILITIES_DIR)
/ToolBase/
\
-I
$(TOOL_DIR)
/intersectFile/
# ----------------------------------
# define our source and object files
...
...
@@ -41,7 +41,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(
D
FLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(
CPP
FLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/intersectFile/Makefile
View file @
2d7b5503
...
...
@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(DFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(DFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/jaccard/Makefile
View file @
2d7b5503
...
...
@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(DFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(DFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
src/linksBed/Makefile
View file @
2d7b5503
...
...
@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling"
$
(
*
F
)
.cpp
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
$(CXX)
-c
-o
$@
$
(
*
F
)
.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(CPPFLAGS)
$(INCLUDES)
clean
:
@
echo
"Cleaning up."
...
...
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