Commit bcffe100 authored by Aaron's avatar Aaron
Browse files

Added groupby back into the bedtools package.

parent 761d4a58
...@@ -29,6 +29,8 @@ SUBDIRS = $(SRC_DIR)/annotateBed \ ...@@ -29,6 +29,8 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/fastaFromBed \ $(SRC_DIR)/fastaFromBed \
$(SRC_DIR)/flankBed \ $(SRC_DIR)/flankBed \
$(SRC_DIR)/genomeCoverageBed \ $(SRC_DIR)/genomeCoverageBed \
$(SRC_DIR)/getOverlap \
$(SRC_DIR)/groupBy \
$(SRC_DIR)/intersectBed \ $(SRC_DIR)/intersectBed \
$(SRC_DIR)/linksBed \ $(SRC_DIR)/linksBed \
$(SRC_DIR)/maskFastaFromBed \ $(SRC_DIR)/maskFastaFromBed \
...@@ -36,7 +38,6 @@ SUBDIRS = $(SRC_DIR)/annotateBed \ ...@@ -36,7 +38,6 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/multiBamCov \ $(SRC_DIR)/multiBamCov \
$(SRC_DIR)/multiIntersectBed \ $(SRC_DIR)/multiIntersectBed \
$(SRC_DIR)/nucBed \ $(SRC_DIR)/nucBed \
$(SRC_DIR)/getOverlap \
$(SRC_DIR)/pairToBed \ $(SRC_DIR)/pairToBed \
$(SRC_DIR)/pairToPair \ $(SRC_DIR)/pairToPair \
$(SRC_DIR)/shuffleBed \ $(SRC_DIR)/shuffleBed \
......
...@@ -21,6 +21,7 @@ def main(): ...@@ -21,6 +21,7 @@ def main():
'flank': 'flankBed', 'flank': 'flankBed',
'genomecov': 'genomeCoverageBed', 'genomecov': 'genomeCoverageBed',
'getfasta': 'fastaFromBed', 'getfasta': 'fastaFromBed',
'groupby': 'groupBy',
'igv': 'bedToIgv', 'igv': 'bedToIgv',
'intersect': 'intersectBed', 'intersect': 'intersectBed',
'links': 'linksBed', 'links': 'linksBed',
......
...@@ -48,6 +48,7 @@ int fastafrombed_main(int argc, char* argv[]);// ...@@ -48,6 +48,7 @@ int fastafrombed_main(int argc, char* argv[]);//
int flank_main(int argc, char* argv[]); // int flank_main(int argc, char* argv[]); //
int genomecoverage_main(int argc, char* argv[]);// int genomecoverage_main(int argc, char* argv[]);//
int getoverlap_main(int argc, char* argv[]);// int getoverlap_main(int argc, char* argv[]);//
int groupby_main(int argc, char* argv[]);//
int intersect_main(int argc, char* argv[]); // int intersect_main(int argc, char* argv[]); //
int links_main(int argc, char* argv[]);// int links_main(int argc, char* argv[]);//
int maskfastafrombed_main(int argc, char* argv[]);// int maskfastafrombed_main(int argc, char* argv[]);//
...@@ -120,7 +121,7 @@ int main(int argc, char *argv[]) ...@@ -120,7 +121,7 @@ int main(int argc, char *argv[])
else if (sub_cmd == "igv") return bedtoigv_main(argc-1, argv+1); else if (sub_cmd == "igv") return bedtoigv_main(argc-1, argv+1);
else if (sub_cmd == "links") return links_main(argc-1, argv+1); else if (sub_cmd == "links") return links_main(argc-1, argv+1);
else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1); else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
else if (sub_cmd == "groupby") return groupby_main(argc-1, argv+1);
// help // help
else if (sub_cmd == "-h" || sub_cmd == "--help" || else if (sub_cmd == "-h" || sub_cmd == "--help" ||
sub_cmd == "-help") sub_cmd == "-help")
...@@ -216,6 +217,7 @@ int bedtools_help(void) ...@@ -216,6 +217,7 @@ int bedtools_help(void)
cout << " igv " << "Create an IGV snapshot batch script.\n"; cout << " igv " << "Create an IGV snapshot batch script.\n";
cout << " links " << "Create a HTML page of links to UCSC locations.\n"; cout << " links " << "Create a HTML page of links to UCSC locations.\n";
cout << " makewindows " << "Make interval \"windows\" across a genome.\n"; cout << " makewindows " << "Make interval \"windows\" across a genome.\n";
cout << " groupby " << "Group by common cols. & summarize oth. cols. (~ SQL \"groupBy\")\n";
cout << endl; cout << endl;
cout << " -General help:\n"; cout << " -General help:\n";
......
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/tabFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= groupBy.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=tabFile.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
.PHONY: all
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/tabFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
.PHONY: clean
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