From f2543820689858382da2f53a946efa4a834456df Mon Sep 17 00:00:00 2001 From: Aaron <aaronquinlan@gmail.com> Date: Sun, 18 Jul 2010 13:45:16 -0400 Subject: [PATCH] Fixed bug in Makefiles calling fileType.o "filetype.o" --- src/bed12ToBed6/Makefile | 2 +- src/bedToBam/Makefile | 4 ++-- src/bedToIgv/Makefile | 2 +- src/closestBed/Makefile | 2 +- src/complementBed/Makefile | 2 +- src/coverageBed/Makefile | 2 +- src/fastaFromBed/Makefile | 2 +- src/genomeCoverageBed/Makefile | 2 +- src/groupBy/Makefile | 2 +- src/intersectBed/Makefile | 2 +- src/linksBed/Makefile | 2 +- src/maskFastaFromBed/Makefile | 2 +- src/mergeBed/Makefile | 2 +- src/overlap/Makefile | 2 +- src/pairToBed/Makefile | 2 +- src/shuffleBed/Makefile | 2 +- src/slopBed/Makefile | 2 +- src/sortBed/Makefile | 2 +- src/subtractBed/Makefile | 2 +- src/windowBed/Makefile | 2 +- 20 files changed, 21 insertions(+), 21 deletions(-) diff --git a/src/bed12ToBed6/Makefile b/src/bed12ToBed6/Makefile index 036bda41..e2e12883 100644 --- a/src/bed12ToBed6/Makefile +++ b/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)/%,$(OBJECTS)) PROGRAM= bed12ToBed6 diff --git a/src/bedToBam/Makefile b/src/bedToBam/Makefile index 946717a7..2d02b52c 100644 --- a/src/bedToBam/Makefile +++ b/src/bedToBam/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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 $(UTILITIES_DIR)/fileType/ clean: @echo "Cleaning up." diff --git a/src/bedToIgv/Makefile b/src/bedToIgv/Makefile index 80970a41..382b8830 100644 --- a/src/bedToIgv/Makefile +++ b/src/bedToIgv/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= bedToIgv diff --git a/src/closestBed/Makefile b/src/closestBed/Makefile index ca4f9bdd..00cfd889 100644 --- a/src/closestBed/Makefile +++ b/src/closestBed/Makefile @@ -11,7 +11,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= closestBed diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile index ec79524b..1e980bd6 100644 --- a/src/complementBed/Makefile +++ b/src/complementBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= complementBed diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile index 2a93031b..722b0c63 100644 --- a/src/coverageBed/Makefile +++ b/src/coverageBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= coverageBed diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile index 57e0b956..cd271426 100644 --- a/src/fastaFromBed/Makefile +++ b/src/fastaFromBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= fastaFromBed diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile index 3f392867..e6f270bc 100644 --- a/src/genomeCoverageBed/Makefile +++ b/src/genomeCoverageBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= genomeCoverageBed diff --git a/src/groupBy/Makefile b/src/groupBy/Makefile index 6a473836..515b92f8 100644 --- a/src/groupBy/Makefile +++ b/src/groupBy/Makefile @@ -13,7 +13,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= groupBy diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile index 35cc43a3..c4e88a5f 100644 --- a/src/intersectBed/Makefile +++ b/src/intersectBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= intersectBed diff --git a/src/linksBed/Makefile b/src/linksBed/Makefile index 2630fd15..75317bf2 100644 --- a/src/linksBed/Makefile +++ b/src/linksBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= linksBed diff --git a/src/maskFastaFromBed/Makefile b/src/maskFastaFromBed/Makefile index f3b5ba40..9b65fc52 100644 --- a/src/maskFastaFromBed/Makefile +++ b/src/maskFastaFromBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= maskFastaFromBed diff --git a/src/mergeBed/Makefile b/src/mergeBed/Makefile index 961a1189..c6a08b6d 100644 --- a/src/mergeBed/Makefile +++ b/src/mergeBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= mergeBed diff --git a/src/overlap/Makefile b/src/overlap/Makefile index a94cf33f..da7da74f 100644 --- a/src/overlap/Makefile +++ b/src/overlap/Makefile @@ -13,7 +13,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= overlap diff --git a/src/pairToBed/Makefile b/src/pairToBed/Makefile index 27f21d71..173975b0 100644 --- a/src/pairToBed/Makefile +++ b/src/pairToBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= pairToBed diff --git a/src/shuffleBed/Makefile b/src/shuffleBed/Makefile index c5ead63e..42e6cf97 100644 --- a/src/shuffleBed/Makefile +++ b/src/shuffleBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= shuffleBed diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile index 2af66e55..ba798c52 100644 --- a/src/slopBed/Makefile +++ b/src/slopBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= slopBed diff --git a/src/sortBed/Makefile b/src/sortBed/Makefile index 5c0eab82..c675e68a 100644 --- a/src/sortBed/Makefile +++ b/src/sortBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= sortBed diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile index 2fd5d2b7..10069702 100644 --- a/src/subtractBed/Makefile +++ b/src/subtractBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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)/%,$(OBJECTS)) PROGRAM= subtractBed diff --git a/src/windowBed/Makefile b/src/windowBed/Makefile index 4f71017e..f0634e44 100644 --- a/src/windowBed/Makefile +++ b/src/windowBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(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 -- GitLab