Commit f2543820 authored by Aaron's avatar Aaron
Browse files

Fixed bug in Makefiles calling fileType.o "filetype.o"

parent 7f513c62
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= bed12ToBed6.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bed12ToBed6
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= bedToBam.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToBam
......@@ -37,7 +37,7 @@ $(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= bedToIgv.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToIgv
......
......@@ -11,7 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= closestMain.cpp closestBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= closestBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= complementMain.cpp complementBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= complementBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= coverageMain.cpp coverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= coverageBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$
# ----------------------------------
SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= fastaFromBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= genomeCoverageBed
......
......@@ -13,7 +13,7 @@ INCLUDES = -I$(UTILITIES_DIR)/tabFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= groupBy.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= groupBy
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= intersectMain.cpp intersectBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= intersectBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= linksMain.cpp linksBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= linksBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$
# ----------------------------------
SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= maskFastaFromBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= mergeMain.cpp mergeBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= mergeBed
......
......@@ -13,7 +13,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= overlap.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= overlap
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITI
# ----------------------------------
SOURCES= pairToBedMain.cpp pairToBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o filetype.o
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= pairToBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= shuffleBedMain.cpp shuffleBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= shuffleBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT
# ----------------------------------
SOURCES= slopBedMain.cpp slopBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= slopBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= sortMain.cpp sortBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= sortBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= subtractMain.cpp subtractBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= subtractBed
......
......@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$
# ----------------------------------
SOURCES= windowMain.cpp windowBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o filetype.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= windowBed
......
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