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

src/bed12ToBed6/Makefile

@@ -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

src/bedToBam/Makefile

@@ -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."

src/bedToIgv/Makefile

@@ -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

src/closestBed/Makefile

@@ -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

src/complementBed/Makefile

@@ -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

src/coverageBed/Makefile

@@ -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

src/fastaFromBed/Makefile

@@ -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

src/genomeCoverageBed/Makefile

@@ -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

src/groupBy/Makefile

@@ -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

src/intersectBed/Makefile

@@ -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

src/linksBed/Makefile

@@ -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

src/maskFastaFromBed/Makefile

@@ -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

src/mergeBed/Makefile

@@ -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

src/overlap/Makefile

@@ -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

src/pairToBed/Makefile

@@ -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

src/shuffleBed/Makefile

@@ -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

src/slopBed/Makefile

@@ -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

src/sortBed/Makefile

@@ -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

src/subtractBed/Makefile

@@ -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

src/windowBed/Makefile

@@ -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