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Makefile and binary type switch script changes; convert2bed intermedi…
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…ate write buffer now resizes as needed for very large conversion tasks; fixed compiler warnings
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@alexpreynolds
alexpreynolds committed Jul 14, 2017
1 parent 73c7724 commit 81c512c
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Showing 25 changed files with 1,157 additions and 819 deletions.
218 changes: 118 additions & 100 deletions Makefile
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4 changes: 2 additions & 2 deletions applications/bed/bedextract/src/Makefile
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Expand Up @@ -6,7 +6,7 @@ LIB2 = $(MAIN)/interfaces/src/utility
LIB3 = $(MAIN)/interfaces/src/data/starch
THISDIR = ${shell pwd}
PARTY3 = ${THISDIR}/$(MAIN)/third-party
OBJDIR = objects${POSTFIX}
OBJDIR = objects_${BINARY_TYPE}
LIBJANSSON = libjansson.a
LIBBZIP2 = libbz2.a
LIBZLIB = libz.a
Expand Down Expand Up @@ -35,7 +35,7 @@ GPROFFLAGS = $(SFLAGS) -O -std=c++11 -Wall -pedantic -pg $(dependen

SOURCE1 = ExtractRows.cpp
BINDIR = ../bin
PROG = bedextract${POSTFIX}
PROG = bedextract-${BINARY_TYPE}

build: $(BINDIR)/$(PROG)
rm -rf ${OBJDIR}
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6 changes: 2 additions & 4 deletions applications/bed/bedextract/src/Makefile.darwin
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@@ -1,5 +1,3 @@
MIN_OSX_VERSION = 10.7

MAIN = ../../../..
MAINAPPDIR = ../..
HEAD = $(MAIN)/interfaces/general-headers
Expand All @@ -8,7 +6,7 @@ LIB2 = $(MAIN)/interfaces/src/utility
LIB3 = $(MAIN)/interfaces/src/data/starch
THISDIR = ${shell pwd}
PARTY3 = ${THISDIR}/$(MAIN)/third-party
OBJDIR = objects_$(ARCH)${POSTFIX}
OBJDIR = objects_$(ARCH)_${BINARY_TYPE}
LIBJANSSON = libjansson.a
LIBBZIP2 = libbz2.a
LIBZLIB = libz.a
Expand Down Expand Up @@ -39,7 +37,7 @@ GPROFFLAGS = -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConsta

SOURCE1 = ExtractRows.cpp
BINDIR = ../bin
PROG = bedextract${POSTFIX}
PROG = bedextract-${BINARY_TYPE}

build: dependencies
$(CXX) -o $(BINDIR)/$(PROG) $(FLAGS) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) ${LIBRARIES} $(SOURCE1)
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4 changes: 2 additions & 2 deletions applications/bed/bedmap/src/Makefile
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Expand Up @@ -19,7 +19,7 @@ LOCALBZIP2INCDIR = ${LOCALBZIP2DIR}
LOCALZLIBDIR = ${PARTY3}/zlib
LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
LOCALZLIBINCDIR = ${LOCALZLIBDIR}
OBJDIR = objects${POSTFIX}
OBJDIR = objects_${BINARY_TYPE}
INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
Expand All @@ -34,7 +34,7 @@ GPROFFLAGS = ${SFLAGS} ${MEGAFLAGS} -pg -O -std=c++11 -Wall -pedantic $

SOURCE1 = Bedmap.cpp
BINDIR = ../bin
PROG = bedmap${POSTFIX}
PROG = bedmap-${BINARY_TYPE}

build: $(BINDIR)/$(PROG)
rm -rf ${OBJDIR}
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6 changes: 2 additions & 4 deletions applications/bed/bedmap/src/Makefile.darwin
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@@ -1,5 +1,3 @@
MIN_OSX_VERSION = 10.7

MAIN = ../../../..
MAINAPPDIR = ../..
HEAD = $(MAIN)/interfaces/general-headers
Expand All @@ -8,7 +6,7 @@ LIB2 = $(MAIN)/interfaces/src/utility
LIB3 = $(MAIN)/interfaces/src/data/starch
THISDIR = ${shell pwd}
PARTY3 = ${THISDIR}/$(MAIN)/third-party
OBJDIR = objects_$(ARCH)${POSTFIX}
OBJDIR = objects_$(ARCH)_${BINARY_TYPE}
LIBJANSSON = libjansson.a
LIBBZIP2 = libbz2.a
LIBZLIB = libz.a
Expand Down Expand Up @@ -38,7 +36,7 @@ GPROFFLAGS = -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConsta

SOURCE1 = Bedmap.cpp
BINDIR = ../bin
PROG = bedmap${POSTFIX}
PROG = bedmap-${BINARY_TYPE}

build: dependencies
$(CXX) -o $(BINDIR)/$(PROG) $(FLAGS) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) ${LIBRARIES} $(SOURCE1)
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4 changes: 2 additions & 2 deletions applications/bed/bedops/src/Makefile
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Expand Up @@ -21,7 +21,7 @@ LOCALBZIP2INCDIR = ${LOCALBZIP2DIR}
LOCALZLIBDIR = ${PARTY3}/zlib
LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
LOCALZLIBINCDIR = ${LOCALZLIBDIR}
OBJDIR = objects${POSTFIX}
OBJDIR = objects_${BINARY_TYPE}
INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
Expand All @@ -35,7 +35,7 @@ DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedops.cpp
BINDIR = ../bin
PROG = bedops${POSTFIX}
PROG = bedops-${BINARY_TYPE}

build: $(BINDIR)/$(PROG)
rm -rf $(OBJDIR)
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6 changes: 2 additions & 4 deletions applications/bed/bedops/src/Makefile.darwin
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@@ -1,5 +1,3 @@
MIN_OSX_VERSION = 10.7

MAIN = ../../../..
MAINAPPDIR = ../..
HEAD = $(MAIN)/interfaces/general-headers
Expand All @@ -22,7 +20,7 @@ LOCALBZIP2INCDIR = ${LOCALBZIP2DIR}
LOCALZLIBDIR = ${PARTY3}/darwin_intel_${ARCH}/zlib
LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
LOCALZLIBINCDIR = ${LOCALZLIBDIR}
OBJDIR = objects_$(ARCH)${POSTFIX}
OBJDIR = objects_$(ARCH)_${BINARY_TYPE}
INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
Expand All @@ -37,7 +35,7 @@ GPROFFLAGS = ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)

SOURCE1 = Bedops.cpp
BINDIR = ../bin
PROG = bedops${POSTFIX}
PROG = bedops-${BINARY_TYPE}

build: dependencies
$(CXX) -o $(BINDIR)/$(PROG) $(FLAGS) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) ${LIBRARIES} $(SOURCE1)
Expand Down
4 changes: 2 additions & 2 deletions applications/bed/closestfeats/src/Makefile
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Expand Up @@ -19,7 +19,7 @@ LOCALBZIP2INCDIR = ${LOCALBZIP2DIR}
LOCALZLIBDIR = ${PARTY3}/zlib
LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
LOCALZLIBINCDIR = ${LOCALZLIBDIR}
OBJDIR = objects${POSTFIX}
OBJDIR = objects_${BINARY_TYPE}
INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
Expand All @@ -33,7 +33,7 @@ DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ClosestFeature.cpp
BINDIR = ../bin
PROG = closest-features${POSTFIX}
PROG = closest-features-${BINARY_TYPE}

build: $(BINDIR)/$(PROG)
rm -rf $(OBJDIR)
Expand Down
6 changes: 2 additions & 4 deletions applications/bed/closestfeats/src/Makefile.darwin
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@@ -1,5 +1,3 @@
MIN_OSX_VERSION = 10.7

MAIN = ../../../..
MAINAPPDIR = ../..
HEAD = $(MAIN)/interfaces/general-headers
Expand All @@ -8,7 +6,7 @@ LIB2 = $(MAIN)/interfaces/src/utility
LIB3 = $(MAIN)/interfaces/src/data/starch
THISDIR = ${shell pwd}
PARTY3 = ${THISDIR}/$(MAIN)/third-party
OBJDIR = objects_$(ARCH)"${POSTFIX}"
OBJDIR = objects_$(ARCH)_${BINARY_TYPE}
LIBJANSSON = libjansson.a
LIBBZIP2 = libbz2.a
LIBZLIB = libz.a
Expand Down Expand Up @@ -38,7 +36,7 @@ GPROFFLAGS = ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)

SOURCE1 = ClosestFeature.cpp
BINDIR = ../bin
PROG = closest-features"${POSTFIX}"
PROG = closest-features-${BINARY_TYPE}

build: dependencies
$(CXX) -o $(BINDIR)/$(PROG) $(FLAGS) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) ${LIBRARIES} $(SOURCE1)
Expand Down
14 changes: 7 additions & 7 deletions applications/bed/conversion/src/Makefile
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Expand Up @@ -6,7 +6,7 @@ CPFLAGS = -pg
LIBS = -lpthread
INCLUDES := -iquote"${CURDIR}"
DISTDIR = ../bin
OBJDIR = objects${POSTFIX}
OBJDIR = objects_${BINARY_TYPE}
WRAPPERDIR = wrappers
PROG = convert2bed
SOURCE = convert2bed.c
Expand All @@ -16,30 +16,30 @@ all: build

.PHONY: build build_debug build_gprof clean

build: $(DISTDIR)/$(PROG)${POSTFIX}
build: $(DISTDIR)/$(PROG)-${BINARY_TYPE}
rm -rf $(OBJDIR)
build_debug: $(DISTDIR)/debug.$(PROG)${POSTFIX}
build_debug: $(DISTDIR)/debug.$(PROG)-${BINARY_TYPE}
rm -rf $(OBJDIR)
build_gprof: $(DISTDIR)/gprof.$(PROG)${POSTFIX}
build_gprof: $(DISTDIR)/gprof.$(PROG)-${BINARY_TYPE}
rm -rf $(OBJDIR)

$(DISTDIR)/$(PROG): $(PROG).c
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)

$(DISTDIR)/%${POSTFIX}: %.c
$(DISTDIR)/%${BINARY_TYPE}: %.c
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)

$(DISTDIR)/debug.$(PROG): $(PROG).c
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CDFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)

$(DISTDIR)/debug.%${POSTFIX}: %.c
$(DISTDIR)/debug.%${BINARY_TYPE}: %.c
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CDFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)

$(DISTDIR)/gprof.$(PROG): $(PROG).c gprof-helper.so
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CPFLAGS) $(SFLAGS) $(INCLUDES) $< -o $@ $(LIBS)
@echo -e "\nNote: To profile convert2bed with gprof/pthreads, run:\n\t$$ LD_PRELOAD=/path/to/gprof-helper.so convert2bed"

$(DISTDIR)/gprof.%${POSTFIX}: %.c gprof-helper.so
$(DISTDIR)/gprof.%${BINARY_TYPE}: %.c gprof-helper.so
mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CPFLAGS) $(SFLAGS) $(INCLUDES) $< -o $@ $(LIBS)
@echo -e "\nNote: To profile convert2bed with gprof/pthreads, run:\n\t$$ LD_PRELOAD=/path/to/gprof-helper.so convert2bed"

Expand Down
14 changes: 8 additions & 6 deletions applications/bed/conversion/src/Makefile.darwin
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@@ -1,13 +1,15 @@
MIN_OSX_VERSION = 10.7
BLDFLAGS = -Wall -Wextra -pedantic -std=c99
COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 ${MEGAFLAGS}
CFLAGS = -O3
CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
CPFLAGS = -pg
LIBS = -lpthread
INCLUDES := -iquote"${CURDIR}"
MAIN = ../../../..
INTERFACES = $(MAIN)/interfaces
HEAD = ${INTERFACES}/general-headers
INCLUDES := -iquote"${CURDIR}" -iquote"${HEAD}"
DISTDIR = ../bin
OBJDIR = objects"${POSTFIX}"
OBJDIR = objects_${BINARY_TYPE}
WRAPPERDIR = wrappers
PROG = convert2bed
SOURCE = convert2bed.c
Expand All @@ -23,18 +25,18 @@ setup:

build: setup
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CFLAGS) -c $(SOURCE) -o $(OBJDIR)/$(PROG).o $(INCLUDES)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/$(PROG)${POSTFIX} $(LIBS)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/$(PROG)-${BINARY_TYPE} $(LIBS)
rm -rf $(OBJDIR)

build_debug: setup
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CDFLAGS) -c $(SOURCE) -o $(OBJDIR)/$(PROG).o $(INCLUDES)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CDFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/debug.$(PROG)${POSTFIX} $(LIBS)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CDFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/debug.$(PROG)-${BINARY_TYPE} $(LIBS)
rm -rf $(OBJDIR)

build_gprof: setup
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) -shared -fPIC gprof-helper.c -o gprof-helper.so $(LIBS) -ldl
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CPFLAGS) -c $(SOURCE) -o $(OBJDIR)/$(PROG).o $(INCLUDES)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CPFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/$(PROG)${POSTFIX} $(LIBS)
$(CC) -mmacosx-version-min=$(MIN_OSX_VERSION) -arch $(ARCH) $(BLDFLAGS) $(COMMONFLAGS) $(CPFLAGS) $(OBJDIR)/$(PROG).o -o $(DISTDIR)/$(PROG)-${BINARY_TYPE} $(LIBS)
@echo "\nNote: To profile convert2bed with gprof/pthreads, run:\n\t$$ LD_PRELOAD=/path/to/gprof-helper.so convert2bed"
rm -rf $(OBJDIR)

Expand Down

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