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Updated overlap usage statement.
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@arq5x
arq5x committed Jul 17, 2010
1 parent 5eaca61 commit a4c6777
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Showing 33 changed files with 128 additions and 59 deletions.
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -14,7 +14,7 @@ export LIBS = -lz
# define our source subdirectories
SUBDIRS = $(SRC_DIR)/bamToBed $(SRC_DIR)/bedToBam $(SRC_DIR)/bedToIgv $(SRC_DIR)/bed12ToBed6 $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/groupBy $(SRC_DIR)/intersectBed $(SRC_DIR)/linksBed $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/mergeBed $(SRC_DIR)/overlap $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/subtractBed $(SRC_DIR)/windowBed

UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/tabFile $(SRC_DIR)/utils/genomeFile $(SRC_DIR)/utils/gzstream $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools
UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/tabFile $(SRC_DIR)/utils/genomeFile $(SRC_DIR)/utils/gzstream $(SRC_DIR)/utils/fileType $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools

all:

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2 changes: 1 addition & 1 deletion src/bamToBed/Makefile
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Expand Up @@ -5,7 +5,7 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/lineFileUtilities/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
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4 changes: 2 additions & 2 deletions src/bed12ToBed6/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= bed12ToBed6.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bed12ToBed6
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4 changes: 2 additions & 2 deletions src/bedToBam/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= bedToBam.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToBam
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4 changes: 2 additions & 2 deletions src/bedToIgv/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= bedToIgv.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToIgv
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5 changes: 2 additions & 3 deletions src/closestBed/Makefile
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Expand Up @@ -5,14 +5,13 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/

INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= closestMain.cpp closestBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= closestBed
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4 changes: 2 additions & 2 deletions src/complementBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= complementMain.cpp complementBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= complementBed
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4 changes: 2 additions & 2 deletions src/coverageBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= coverageMain.cpp coverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= coverageBed
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4 changes: 2 additions & 2 deletions src/fastaFromBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= fastaFromBed
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4 changes: 2 additions & 2 deletions src/genomeCoverageBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= genomeCoverageBed
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4 changes: 2 additions & 2 deletions src/groupBy/Makefile
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Expand Up @@ -6,14 +6,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/tabFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/tabFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= groupBy.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= groupBy
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4 changes: 2 additions & 2 deletions src/intersectBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= intersectMain.cpp intersectBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= intersectBed
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4 changes: 2 additions & 2 deletions src/linksBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= linksMain.cpp linksBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= linksBed
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4 changes: 2 additions & 2 deletions src/maskFastaFromBed/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= maskFastaFromBed
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5 changes: 3 additions & 2 deletions src/mergeBed/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= mergeMain.cpp mergeBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= mergeBed
Expand All @@ -34,6 +34,7 @@ $(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/

clean:
@echo "Cleaning up."
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4 changes: 2 additions & 2 deletions src/overlap/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= overlap.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= overlap
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4 changes: 2 additions & 2 deletions src/overlap/overlap.cpp
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Expand Up @@ -133,10 +133,10 @@ void ShowHelp(void) {
cerr << "\t\tstart1,end1,start2,end2" << endl << endl;

cerr << "Example: " << endl;
cerr << "\t$ cat test.out" << endl;
cerr << "\t$ windowBed -a A.bed -b B.bed -w 10" << endl;
cerr << "\tchr1 10 20 A chr1 15 25 B" << endl;
cerr << "\tchr1 10 20 C chr1 25 35 D" << endl << endl;
cerr << "\t$ cat test.out | overlaps -i stdin -cols 2,3,6,7" << endl;
cerr << "\t$ windowBed -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7" << endl;
cerr << "\tchr1 10 20 A chr1 15 25 B 5" << endl;
cerr << "\tchr1 10 20 C chr1 25 35 D -5" << endl;

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4 changes: 2 additions & 2 deletions src/pairToBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= pairToBedMain.cpp pairToBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= pairToBed
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4 changes: 2 additions & 2 deletions src/pairToPair/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= pairToPairMain.cpp pairToPair.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= pairToPair
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4 changes: 2 additions & 2 deletions src/shuffleBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= shuffleBedMain.cpp shuffleBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= shuffleBed
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4 changes: 2 additions & 2 deletions src/slopBed/Makefile
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Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= slopBedMain.cpp slopBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= slopBed
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4 changes: 2 additions & 2 deletions src/sortBed/Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/

# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= sortMain.cpp sortBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= sortBed
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