New upstream version 0.6.8-pre3

.dub/

dub.selections.json

BioD/

BioD

./BioD

undeaD/

lz4/

core

bin/

test*

build/

shunit*

/*.sam

/*.cram

/*.crai

/*.txt

*.hex

*.zcat

*.out

/utils/ldc_version_info_.d

profile.data

profile.raw

[submodule "BioD"]

	path = BioD

	url = https://github.com/biod/BioD.git

[submodule "htslib"]

	path = htslib

	url = https://github.com/lomereiter/htslib.git

[submodule "lz4"]

	path = lz4

	url = https://github.com/Cyan4973/lz4

[submodule "undeaD"]

	path = undeaD

	url = https://github.com/dlang/undeaD

[submodule "BioD"]

	path = BioD

	url = https://github.com/biod/BioD.git

[submodule "lz4"]

	path = lz4

	url = https://github.com/lz4/lz4.git

language: d

d:

  - ldc

matrix:

  # OSX testing is under development

  allow_failures:

    - os: osx

  include:

    - os: linux

      compiler: gcc

      addons:

        apt:

          packages:

            # Our dev environment is a more recent GNU C++

            # note that Debian liblz4-dev no longer supports LZ4 frames

            # - liblz4-dev

            - shunit2

    - os: osx

      compiler: clang

script:

  - make

  # - make test - disable tests because shunit2 we use is older

 No newline at end of file

# INSTALL SAMBAMBA

## Sambamba dependencies

* D compiler

* gcc tool chain

* BioD

* htslib

* undeaD

* libz

* liblz4

D_COMPILER=dmd

D_FLAGS=--compiler=dmd -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial

LDMD=ldmd2

# This is a minimalistic make file to build sambamba with ldc2 as per instructions on

# https://github.com/biod/sambamba#compiling-sambamba

#

# Typical usage:

#

#    make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib debug|profile|release|static

#

# Static release with optimization (for releases):

#

#   make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib pgo-static

#

# Debug version

#

#   make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib debug

STATIC_LIB_PATH=-Lhtslib -Llz4/lib

STATIC_LIB_SUBCMD=$(STATIC_LIB_PATH) -Wl,-Bstatic -lhts -llz4 -Wl,-Bdynamic

RDMD_FLAGS=--force --build-only --compiler=$(D_COMPILER) $(D_FLAGS)

D_COMPILER=ldc2

DFLAGS      = -wi -I. -IBioD -IundeaD/src -g

PLATFORM := $(shell uname -s)

DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a

DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a

LIBS        = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lrt -L-lpthread -L-lm

LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a

SRC         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio2/*.d BioD/bio2/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)

OBJ         = $(SRC:.d=.o) utils/ldc_version_info_.o

OUT         = bin/sambamba

ifeq "$(PLATFORM)" "Darwin"

STATIC_LIB_PATH=-Lhtslib -Llz4

LINK_CMD=gcc -dead_strip -lphobos2-ldc -ldruntime-ldc -lm -lpthread htslib/libhts.a lz4/lib/liblz4.a build/sambamba.o -o build/sambamba

DMD_STATIC_LIBS=htslib/libhts.a lz4/lib/liblz4.a

.PHONY: all debug release static clean test

define split-debug

dsymutil build/sambamba -o build/sambamba.dSYM

strip -S build/sambamba

endef

debug:                             DFLAGS += -O0 -d-debug -link-debuglib

else

profile:                           DFLAGS += -fprofile-instr-generate=profile.raw

LINK_CMD=gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o $(STATIC_LIB_SUBCMD) -lphobos2-ldc -ldruntime-ldc  -lrt -lpthread -lm -ldl

DMD_STATIC_LIBS=-L-Lhtslib -L-l:libhts.a -L-l:libphobos2.a -L-Llz4/lib -L-l:liblz4.a

release static profile pgo-static: DFLAGS += -O3 -release -enable-inlining -boundscheck=off

define split-debug

objcopy --only-keep-debug build/sambamba sambamba.debug

objcopy --strip-debug build/sambamba

objcopy --add-gnu-debuglink=sambamba.debug build/sambamba

mv sambamba.debug build/

endef

static:                            DFLAGS += -static -L-Bstatic

endif

pgo-static:                        DFLAGS += -fprofile-instr-use=profile.data

PREREQS := ldc-version-info htslib-static lz4-static

all: release

# DMD only - this goal is used because of fast compilation speed, during development

all: $(PREREQS)

	mkdir -p build/

	rdmd --force --build-only $(D_FLAGS) $(DMD_STATIC_LIBS) -ofbuild/sambamba main.d

lz4-static: lz4/lib/liblz4.a

# This is the main Makefile goal, used for building releases (best performance)

sambamba-ldmd2-64: $(PREREQS)

	mkdir -p build/

	$(LDMD) @sambamba-ldmd-release.rsp

	$(LINK_CMD)

	$(split-debug)

lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c

	cd lz4/lib && gcc -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && $(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o

# For debugging; GDB & Valgrind are more friendly to executables created using LDC/GDC than DMD

sambamba-ldmd2-debug: $(PREREQS)

	mkdir -p build/

	$(LDMD) @sambamba-ldmd-debug.rsp

	$(LINK_CMD)

htslib-static:

	cd htslib && $(MAKE)

ldc-version-info:

	./gen_ldc_version_info.py $(shell which $(LDMD)) > utils/ldc_version_info_.d

	./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d

	cat utils/ldc_version_info_.d

htslib-static:

	cd htslib && $(MAKE)

utils/ldc_version_info_.o: ldc-version-info

	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)

lz4-static: lz4/lib/liblz4.a

build-setup: lz4-static htslib-static ldc-version-info

	mkdir -p bin/

lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c

	cd lz4/lib && $(CC) -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && $(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o

default debug release static: $(OUT)

# all below link to libhts dynamically for simplicity

profile: release

	./bin/sambamba sort /gnu/data/in_raw.bam -p > /dev/null

	ldc-profdata merge -output=profile.data profile.raw

	rm ./bin/sambamba ./bin/sambamba.o # trigger rebuild

sambamba-flagstat:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-flagstat sambamba/flagstat.d

default: all

sambamba-merge:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-merge sambamba/merge.d

# ---- Compile step

%.o: %.d

	$(D_COMPILER) $(DFLAGS) -c $< -od=$(dir $@)

sambamba-index:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-index sambamba/index.d

singleobj:

	$(info compile single object...)

	$(D_COMPILER) -singleobj $(DFLAGS) -c -of=bin/sambamba.o $(SRC)

sambamba-sort:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-sort sambamba/sort.d

# ---- Link step

$(OUT): build-setup singleobj utils/ldc_version_info_.o

	$(info linking...)

	$(D_COMPILER) $(DFLAGS) -of=bin/sambamba bin/sambamba.o utils/ldc_version_info_.o $(LIBS)

sambamba-view:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-view sambamba/view.d

test:

	./run_tests.sh

sambamba-slice:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-slice sambamba/slice.d

check: test

sambamba-markdup:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-markdup sambamba/markdup.d

debug-strip:

	objcopy --only-keep-debug bin/sambamba sambamba.debug

	objcopy --strip-debug bin/sambamba

	objcopy --add-gnu-debuglink=sambamba.debug bin/sambamba

	mv sambamba.debug bin/

sambamba-depth:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-depth sambamba/depth.d

pgo-static: profile static debug-strip

sambamba-pileup:

	mkdir -p build/

	rdmd $(RDMD_FLAGS) -L-lhts -version=standalone -ofbuild/sambamba-pileup sambamba/pileup.d

install:

	install -m 0755 bin/sambamba $(prefix)/bin

.PHONY: clean ldc-version-info

clean: clean-d

	cd htslib ; make clean

	rm -f profile.data

	rm -f profile.raw

clean:

	rm -rf build/ ; $(MAKE) -C htslib clean ; $(MAKE) -C lz4 clean

clean-d:

	rm -rf bin/*

	rm -f $(OBJ) $(OUT) trace.{def,log}